############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PloGO2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PloGO2_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PloGO2.Rcheck' * using R version 4.1.1 (2021-08-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'PloGO2/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PloGO2' version '1.4.0' * 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 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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 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 files in 'vignettes' ... NOTE The following files look like leftovers/mistakes: 'Rplots.pdf' Please remove them from your package. * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PloGO 43.55 0.36 44.18 abundancePlot 21.71 1.03 23.30 getGoID 22.20 0.00 22.21 writeAnnotation 21.39 0.12 21.52 processAnnotation 20.56 0.19 20.83 processGoFile 10.91 0.00 10.90 ExcelToPloPathway 4.63 0.79 5.85 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed PloGO 41.77 0.30 42.07 writeAnnotation 21.75 0.00 21.75 processAnnotation 20.50 0.22 20.71 getGoID 19.49 0.00 19.48 abundancePlot 17.72 1.09 18.86 processGoFile 11.33 0.00 11.33 ExcelToPloPathway 5.31 0.72 6.14 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PloGO2.Rcheck/00check.log' for details.