############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ROntoTools_2.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ROntoTools.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * using platform: x86_64-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 Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ROntoTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ROntoTools’ version ‘2.31.0’ * 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 ‘ROntoTools’ 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 ... NOTE Problems with news in ‘NEWS’: Cannot process chunk/lines: action between the genes (as edgeWeights) and the relevance of each gene (as Cannot process chunk/lines: weights to be used as nodeWeights * 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 ... NOTE Warning: no function found corresponding to methods exports from ‘ROntoTools’ for: ‘Summary’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Packages in Depends field not imported from: ‘Rgraphviz’ ‘methods’ 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 ... NOTE KEGGpathway2Graph: no visible global function definition for ‘is’ KEGGpathway2Graph: no visible global function definition for ‘new’ compute.B: no visible global function definition for ‘as’ compute.B_pDis: no visible global function definition for ‘as’ compute.normalInv: no visible global function definition for ‘pnorm’ compute.normalInv: no visible binding for global variable ‘qnorm’ compute.pORA: no visible global function definition for ‘phyper’ get.totalAccNorm: no visible global function definition for ‘sd’ get.totalPertNorm: no visible global function definition for ‘sd’ get.totalpDisNorm: no visible global function definition for ‘sd’ graph2ftM: no visible global function definition for ‘as’ keggPathwayGraphs: no visible global function definition for ‘txtProgressBar’ keggPathwayGraphs : : no visible global function definition for ‘new’ keggPathwayGraphs : : no visible global function definition for ‘setTxtProgressBar’ keggPathwayGraphs : : no visible global function definition for ‘getTxtProgressBar’ loadKEGGpathwayDataREST: no visible global function definition for ‘txtProgressBar’ loadKEGGpathwayDataREST : : no visible global function definition for ‘setTxtProgressBar’ loadKEGGpathwayDataREST : : no visible global function definition for ‘getTxtProgressBar’ pDis.boot: no visible global function definition for ‘new’ pDis.helper: no visible global function definition for ‘txtProgressBar’ pDis.helper : : no visible global function definition for ‘setTxtProgressBar’ pDis.helper : : no visible global function definition for ‘getTxtProgressBar’ pDis.helper: no visible global function definition for ‘new’ pe.boot: no visible global function definition for ‘new’ peEdgeRenderInfo: no visible global function definition for ‘removedEdges’ peNodeRenderInfo: no visible global function definition for ‘slot’ peNodeRenderInfo: no visible global function definition for ‘colorRampPalette’ pf.helper: no visible global function definition for ‘txtProgressBar’ pf.helper : : no visible global function definition for ‘setTxtProgressBar’ pf.helper : : no visible global function definition for ‘getTxtProgressBar’ pf.helper: no visible global function definition for ‘new’ subGraphByNodeType: no visible global function definition for ‘new’ summary.pDisRes : : no visible global function definition for ‘p.adjust’ summary.peRes : : no visible global function definition for ‘p.adjust’ plot,pePathway-character: no visible global function definition for ‘slot’ plot,pePathway-character: no visible global function definition for ‘abline’ plot,pePathway-character: no visible global function definition for ‘points’ plot,pePathway-character: no visible global function definition for ‘sd’ plot,pePathway-character: no visible global function definition for ‘density’ plot,peRes-character: no visible global function definition for ‘Summary’ plot,peRes-character: no visible global function definition for ‘chull’ plot,peRes-character: no visible global function definition for ‘polygon’ plot,peRes-character: no visible global function definition for ‘points’ plot,peRes-character: no visible global function definition for ‘text’ plot,peRes-character: no visible global function definition for ‘abline’ Undefined global functions or variables: Summary abline as chull colorRampPalette density getTxtProgressBar is new p.adjust phyper pnorm points polygon qnorm removedEdges sd setTxtProgressBar slot text txtProgressBar Consider adding importFrom("grDevices", "chull", "colorRampPalette") importFrom("graphics", "abline", "points", "polygon", "text") importFrom("methods", "Summary", "as", "is", "new", "slot") importFrom("stats", "density", "p.adjust", "phyper", "pnorm", "qnorm", "sd") importFrom("utils", "getTxtProgressBar", "setTxtProgressBar", "txtProgressBar") 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 ... WARNING Codoc mismatches from Rd file 'compute.fisher.Rd': compute.fisher Code: function(p, eps = 1e-24) Docs: function(p, eps = 1e-06) Mismatches in argument default values: Name: 'eps' Code: 1e-24 Docs: 1e-06 * checking Rd \usage sections ... NOTE S3 methods shown with full name in Rd file 'summary.pDisRes.Rd': ‘summary.pDisRes’ S3 methods shown with full name in Rd file 'summary.peRes.Rd': ‘summary.peRes’ The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 plot.peRes-methods 19.774 0.278 25.265 peNodeRenderInfo 15.704 0.236 19.027 peEdgeRenderInfo 14.764 0.188 17.798 plot.pePathway-methods 14.074 0.227 17.647 summary.peRes 13.952 0.203 17.271 pe 13.826 0.220 16.806 pDis 13.391 0.256 16.181 summary.pDisRes 12.509 0.209 15.754 setEdgeWeights 4.145 0.092 5.228 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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 WARNING, 5 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ROntoTools.Rcheck/00check.log’ for details.