############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:gage.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings gage_2.42.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/gage.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘gage/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘gage’ version ‘2.42.0’ * 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 ‘gage’ 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 * 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 ... WARNING '::' or ':::' import not declared from: ‘BiocManager’ 'loadNamespace' or 'requireNamespace' call not declared from: ‘BiocManager’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE colorpanel: no visible global function definition for ‘col2rgb’ colorpanel: no visible global function definition for ‘rgb’ deComp: no visible global function definition for ‘annot.db’ deComp: no visible global function definition for ‘write.table’ eg2sym: no visible binding for global variable ‘egSymb’ essGene: no visible binding for global variable ‘sd’ essGene: no visible global function definition for ‘qchisq’ esset.grp: no visible global function definition for ‘sd’ esset.grp : : no visible global function definition for ‘phyper’ esset.grp: no visible global function definition for ‘as’ esset.grp: no visible global function definition for ‘write.table’ esset.grp: no visible global function definition for ‘nodes’ esset.grp: no visible global function definition for ‘edgeNames’ esset.grp: no visible global function definition for ‘pdf’ esset.grp: no visible global function definition for ‘make.graph’ esset.grp : : no visible global function definition for ‘nodes’ esset.grp: no visible global function definition for ‘points’ esset.grp: no visible global function definition for ‘dev.off’ gageComp: no visible global function definition for ‘pdf’ gageComp: no visible global function definition for ‘dev.off’ gagePipe: no visible global function definition for ‘write.table’ gagePipe: no visible global function definition for ‘pdf’ gagePipe: no visible global function definition for ‘dev.off’ gagePrep : : no visible global function definition for ‘t.test’ gageSum: no visible global function definition for ‘qnorm’ gageSum: no visible global function definition for ‘pnorm’ gageSum: no visible global function definition for ‘aggregate’ gageSum : : no visible global function definition for ‘pnorm’ gageSum: no visible global function definition for ‘pgamma’ gageSum: no visible global function definition for ‘p.adjust’ geneData: no visible global function definition for ‘write.table’ geneData: no visible global function definition for ‘pdf’ geneData: no visible global function definition for ‘dev.off’ geneData: no visible global function definition for ‘par’ geneData: no visible global function definition for ‘abline’ geneData: no visible global function definition for ‘points’ geneData: no visible global function definition for ‘legend’ go.gsets: no visible global function definition for ‘data’ go.gsets: no visible global function definition for ‘install.packages’ gs.KSTest : : no visible global function definition for ‘ks.test’ gs.tTest: no visible binding for global variable ‘sd’ gs.tTest: no visible global function definition for ‘pt’ gs.zTest: no visible binding for global variable ‘sd’ gs.zTest: no visible global function definition for ‘pnorm’ heatmap2: no visible binding for global variable ‘dist’ heatmap2: no visible binding for global variable ‘hclust’ heatmap2: no visible global function definition for ‘par’ heatmap2: no visible global function definition for ‘median’ heatmap2: no visible binding for global variable ‘sd’ heatmap2: no visible global function definition for ‘order.dendrogram’ heatmap2: no visible global function definition for ‘as.dendrogram’ heatmap2: no visible global function definition for ‘reorder’ heatmap2: no visible global function definition for ‘layout’ heatmap2: no visible global function definition for ‘image’ heatmap2: no visible global function definition for ‘axis’ heatmap2: no visible global function definition for ‘mtext’ heatmap2: no visible global function definition for ‘rect’ heatmap2: no visible global function definition for ‘abline’ heatmap2: no visible global function definition for ‘lines’ heatmap2: no visible global function definition for ‘text’ heatmap2: no visible global function definition for ‘plot.new’ heatmap2: no visible global function definition for ‘title’ heatmap2: no visible global function definition for ‘density’ heatmap2: no visible global function definition for ‘hist’ kegg.gsets: no visible global function definition for ‘data’ kegg.gsets: no visible binding for global variable ‘khier’ kegg.species.code: no visible global function definition for ‘data’ kegg.species.code: no visible binding for global variable ‘korg.1’ readExpData: no visible global function definition for ‘read.delim’ rownorm : : no visible global function definition for ‘sd’ sigGeneSet: no visible global function definition for ‘pdf’ sigGeneSet: no visible global function definition for ‘dev.off’ sym2eg: no visible binding for global variable ‘egSymb’ vennDiagram2: no visible global function definition for ‘is’ vennDiagram2: no visible global function definition for ‘par’ vennDiagram2: no visible global function definition for ‘lines’ vennDiagram2: no visible global function definition for ‘text’ vennDiagram2: no visible global function definition for ‘rect’ vennDiagram2 : printing: no visible global function definition for ‘text’ Undefined global functions or variables: abline aggregate annot.db as as.dendrogram axis col2rgb data density dev.off dist edgeNames egSymb hclust hist image install.packages is khier korg.1 ks.test layout legend lines make.graph median mtext nodes order.dendrogram p.adjust par pdf pgamma phyper plot.new pnorm points pt qchisq qnorm read.delim rect reorder rgb sd t.test text title write.table Consider adding importFrom("grDevices", "col2rgb", "dev.off", "pdf", "rgb") importFrom("graphics", "abline", "axis", "hist", "image", "layout", "legend", "lines", "mtext", "par", "plot.new", "points", "rect", "text", "title") importFrom("methods", "as", "is") importFrom("stats", "aggregate", "as.dendrogram", "density", "dist", "hclust", "ks.test", "median", "order.dendrogram", "p.adjust", "pgamma", "phyper", "pnorm", "pt", "qchisq", "qnorm", "reorder", "sd", "t.test") importFrom("utils", "data", "install.packages", "read.delim", "write.table") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed kegg.gsets 0.619 0.006 11.062 * 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: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/gage.Rcheck/00check.log’ for details.