############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ROntoTools.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ROntoTools_2.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ROntoTools.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘ROntoTools/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ROntoTools’ version ‘2.34.0’ * 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 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 ... 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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed plot.peRes-methods 7.507 0.003 7.511 peNodeRenderInfo 7.094 0.011 7.106 peEdgeRenderInfo 6.404 0.012 6.417 plot.pePathway-methods 6.126 0.003 6.129 summary.peRes 6.084 0.020 6.104 pe 5.949 0.018 5.968 pDis 5.631 0.029 5.660 summary.pDisRes 5.549 0.004 5.554 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/ROntoTools.Rcheck/00check.log’ for details.