############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PloGO2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PloGO2_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘PloGO2/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘PloGO2’ version ‘1.16.0’ * 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 ‘PloGO2’ 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 whether startup messages can be suppressed ... 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 ... NOTE Children: no visible global function definition for ‘Ontology’ ExcelToPloGO: no visible binding for global variable ‘Term’ ExcelToPloGO: no visible binding for global variable ‘Ontology’ GOGraphWrapper: no visible global function definition for ‘Ontology’ GOParent: no visible global function definition for ‘Ontology’ GOTermList: no visible global function definition for ‘Ontology’ PloGO: no visible global function definition for ‘read.delim’ PloGO: no visible global function definition for ‘unzip’ PloGO: no visible global function definition for ‘read.csv’ PloPathway: no visible global function definition for ‘unzip’ PloPathway : : no visible global function definition for ‘read.table’ PloPathway: no visible global function definition for ‘read.csv’ abundancePlot: no visible binding for global variable ‘eps’ aggregateAbundance : : no visible global function definition for ‘Term’ aggregateAbundance : : no visible global function definition for ‘aggregate’ annotationPlot : : no visible global function definition for ‘Term’ compareAnnot: no visible global function definition for ‘fisher.test’ compareAnnot : : no visible global function definition for ‘Term’ compareAnnot: no visible global function definition for ‘p.adjust’ countAndAbundance: no visible global function definition for ‘par’ countAndAbundance: no visible global function definition for ‘barplot’ countAndAbundance: no visible global function definition for ‘axTicks’ countAndAbundance: no visible global function definition for ‘axis’ countAndAbundance: no visible global function definition for ‘title’ genAnnotationFiles: no visible global function definition for ‘read.csv’ genAnnotationFiles: no visible global function definition for ‘write.table’ genWegoFile: no visible global function definition for ‘useMart’ genWegoFile: no visible global function definition for ‘useDataset’ genWegoFile: no visible global function definition for ‘getBM’ genWegoFile: no visible global function definition for ‘aggregate’ genWegoFile: no visible global function definition for ‘write.table’ getGoID: no visible binding for global variable ‘Term’ getUniprotBatch: no visible binding for global variable ‘IDList’ inGraph: no visible global function definition for ‘nodes’ plotAbundanceBar: no visible global function definition for ‘par’ plotAbundanceBar: no visible global function definition for ‘barplot’ plotAbundanceBar: no visible global function definition for ‘rainbow’ plotAbundanceBar: no visible global function definition for ‘legend’ plotMat: no visible global function definition for ‘colorRampPalette’ plotMat : : no visible global function definition for ‘Term’ processAnnotFile: no visible global function definition for ‘read.csv’ processGoFile : : no visible global function definition for ‘Term’ processGoFile: no visible global function definition for ‘read.csv’ processPathFile: no visible global function definition for ‘read.csv’ read.annot.file: no visible global function definition for ‘read.table’ read.annot.file: no visible global function definition for ‘aggregate’ tabulateAnnot : : no visible global function definition for ‘Term’ writeGOannot: no visible global function definition for ‘read.csv’ writeGOannot: no visible global function definition for ‘write.csv’ writeGOannot: no visible global function definition for ‘write.table’ Undefined global functions or variables: IDList Ontology Term aggregate axTicks axis barplot colorRampPalette eps fisher.test getBM legend nodes p.adjust par rainbow read.csv read.delim read.table title unzip useDataset useMart write.csv write.table Consider adding importFrom("grDevices", "colorRampPalette", "rainbow") importFrom("graphics", "axTicks", "axis", "barplot", "legend", "par", "title") importFrom("stats", "aggregate", "fisher.test", "p.adjust") importFrom("utils", "read.csv", "read.delim", "read.table", "unzip", "write.csv", "write.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... 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 R/sysdata.rda ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PloGO 45.241 2.458 62.971 processAnnotation 27.732 0.896 37.495 writeAnnotation 24.055 1.089 33.816 abundancePlot 23.733 0.958 32.425 getGoID 20.994 0.183 30.069 processGoFile 12.673 0.282 16.495 ExcelToPloPathway 3.427 0.722 6.423 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.19-bioc/meat/PloGO2.Rcheck/00check.log’ for details.