################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:MAIT.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings MAIT_1.44.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MAIT.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘MAIT/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘MAIT’ version ‘1.44.0’* 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 for sufficient/correct file permissions ... OK* checking whether package ‘MAIT’ can be installed ... OK* checking installed package size ... OK* checking package directory ... 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 dependencies in R code ... NOTE'library' or 'require' call to ‘rgl’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual.* checking S3 generic/method consistency ... OK* checking replacement functions ... OK* checking foreign function calls ... OK* checking R code for possible problems ... NOTEBiotransformations: no visible global function definition for ‘data’Biotransformations: no visible binding for global variable ‘MAITtables’Biotransformations: no visible global function definition for ‘read.csv’Biotransformations: no visible global function definition for ‘read.csv2’PLSDA: no visible global function definition for ‘predict’Validation: no visible global function definition for ‘predict’Validation: no visible global function definition for ‘sd’Validation: no visible global function definition for ‘rainbow’Validation: no visible global function definition for ‘png’Validation: no visible global function definition for ‘boxplot’Validation: no visible global function definition for ‘legend’Validation: no visible global function definition for ‘title’Validation: no visible global function definition for ‘dev.off’Validation: no visible binding for global variable ‘sd’computeSpectra: no visible global function definition for ‘cor’identifyMetabolites: no visible global function definition for ‘data’identifyMetabolites: no visible binding for global variable ‘MAITtables’identifyMetabolites: no visible global function definition for ‘read.csv’identifyMetabolites: no visible global function definition for ‘write.table’metaboliteTable: no visible global function definition for ‘write.table’peakAggregation: no visible global function definition for ‘write.table’peakAnnotation: no visible global function definition for ‘data’peakAnnotation: no visible binding for global variable ‘MAITtables’peakAnnotation: no visible global function definition for ‘read.csv2’plotBoxplot: no visible global function definition for ‘png’plotBoxplot: no visible global function definition for ‘boxplot’plotBoxplot: no visible global function definition for ‘title’plotBoxplot: no visible global function definition for ‘dev.off’plotHeatmap: no visible global function definition for ‘p.adjust’plotHeatmap : distCor: no visible global function definition for ‘as.dist’plotHeatmap : distCor: no visible global function definition for ‘cor’plotHeatmap : hclustWard: no visible global function definition for ‘hclust’plotHeatmap: no visible global function definition for ‘colorRampPalette’plotHeatmap: no visible global function definition for ‘png’plotHeatmap: no visible global function definition for ‘legend’plotHeatmap: no visible global function definition for ‘dev.off’plotPCA: no visible global function definition for ‘prcomp’plotPCA: no visible global function definition for ‘png’plotPCA: no visible global function definition for ‘legend’plotPCA: no visible global function definition for ‘dev.off’plotPLS: no visible global function definition for ‘png’plotPLS: no visible global function definition for ‘legend’plotPLS: no visible global function definition for ‘dev.off’sigPeaksTable: no visible global function definition for ‘p.adjust’sigPeaksTable: no visible global function definition for ‘aggregate’sigPeaksTable: no visible binding for global variable ‘median’sigPeaksTable: no visible global function definition for ‘write.csv’spectralAnova: no visible global function definition for ‘lm’spectralAnova: no visible global function definition for ‘anova’spectralAnova: no visible global function definition for ‘p.adjust’spectralFUN: no visible global function definition for ‘p.adjust’spectralKruskal: no visible global function definition for ‘kruskal.test’spectralKruskal: no visible global function definition for ‘p.adjust’spectralTStudent: no visible global function definition for ‘lm’spectralTStudent: no visible global function definition for ‘t.test’spectralTStudent: no visible global function definition for ‘p.adjust’spectralWelch: no visible global function definition for ‘lm’spectralWelch: no visible global function definition for ‘t.test’spectralWelch: no visible global function definition for ‘p.adjust’spectralWilcox: no visible global function definition for ‘lm’spectralWilcox: no visible global function definition for ‘wilcox.test’spectralWilcox: no visible global function definition for ‘p.adjust’writeExcelTable: no visible global function definition for ‘write.csv’writeParameterTable: no visible global function definition for ‘write.csv’Undefined global functions or variables: MAITtables aggregate anova as.dist boxplot colorRampPalette cor data dev.off hclust kruskal.test legend lm median p.adjust png prcomp predict rainbow read.csv read.csv2 sd t.test title wilcox.test write.csv write.tableConsider adding importFrom("grDevices", "colorRampPalette", "dev.off", "png", "rainbow") importFrom("graphics", "boxplot", "legend", "title") importFrom("stats", "aggregate", "anova", "as.dist", "cor", "hclust", "kruskal.test", "lm", "median", "p.adjust", "prcomp", "predict", "sd", "t.test", "wilcox.test") importFrom("utils", "data", "read.csv", "read.csv2", "write.csv", "write.table")to your NAMESPACE file.* checking Rd files ... NOTEcheckRd: (-1) classes.Rd:5: Lost braces 5 | Function \code{classes} extracts the class names of a link{MAIT-class} object as a vector. | ^checkRd: (-1) parameters.Rd:5: Lost braces 5 | Function \code{parameters} extracts the slot link{MAIT.Parameters-class} of a \code{\link{MAIT-class}} object. This class contains all the parameters that have been used in the previous functions. Typing a summary of this object, a matrix version of the parameters is obtained. | ^* checking Rd metadata ... OK* checking Rd cross-references ... NOTEFound the following Rd file(s) with Rd \link{} targets missing packageanchors: MAIT-class.Rd: xsAnnotate MAIT.FeatureData-class.Rd: xsAnnotate MAIT.FeatureInfo-class.Rd: xsAnnotate MAIT.PhenoData-class.Rd: xsAnnotate MAIT.RawData-class.Rd: xsAnnotate MAIT.Validation-class.Rd: xsAnnotate peakAnnotation.Rd: xsAnnotate, groupCorr, xsAnnotate-class rawData.Rd: xsAnnotate, xsAnnotate-classPlease provide package anchors for all Rd \link{} targets not in thepackage itself and the base packages.* 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 data for ASCII and uncompressed saves ... OK* checking files in ‘vignettes’ ... OK* checking examples ... OKExamples with CPU (user + system) or elapsed time > 5s user system elapsedovClassifRatio 11.812 0.184 12.011parameters 11.682 0.036 11.718Validation 10.943 0.231 11.257classifRatioClasses 10.930 0.134 11.064ovClassifRatioTable 10.319 0.046 10.365* checking for unstated dependencies in vignettes ... OK* checking package vignettes ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 4 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/MAIT.Rcheck/00check.log’for details.################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL MAIT###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘MAIT’ ...** this is package ‘MAIT’ version ‘1.44.0’** using staged installation** R** data** inst** byte-compile and prepare package for lazy loadingCreating a new generic function for ‘scores’ in package ‘MAIT’Creating a new generic function for ‘loadings’ in package ‘MAIT’** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (MAIT)
