############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:GeneAnswers.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings GeneAnswers_2.36.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GeneAnswers/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘GeneAnswers’ version ‘2.36.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'igraph', 'KEGGREST', 'RCurl', 'annotate', 'Biobase', 'XML', 'RSQLite', 'MASS', 'Heatplus', 'RColorBrewer' Adding so many packages to the search path is excessive and importing selectively is preferable. * 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 ‘GeneAnswers’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'GeneAnswers' is deprecated and will be removed from Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘GeneAnswers’ Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘GeneAnswers’ See ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00install.out’ for details. * checking installed package size ... NOTE installed size is 34.2Mb sub-directories of 1Mb or more: External 32.4Mb data 1.0Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘annotate’ A package should be listed in only one of these fields. * 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 ... NOTE 'library' or 'require' calls to packages already attached by Depends: ‘Biobase’ ‘Heatplus’ ‘KEGGREST’ ‘MASS’ ‘RColorBrewer’ ‘XML’ ‘igraph’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘GO.db’ ‘biomaRt’ ‘reactome.db’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘GeneAnswers/R/zzz.R’: .onLoad calls: require(Biobase) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. getHomoGeneIDs: no visible global function definition for ‘useMart’ getHomoGeneIDs: no visible global function definition for ‘getLDS’ getTotalGeneNumber: no visible global function definition for ‘count.mappedkeys’ getTotalGeneNumber: no visible global function definition for ‘toTable’ getTotalGeneNumber: no visible binding for global variable ‘reactomePATHNAME2ID’ Undefined global functions or variables: count.mappedkeys getLDS reactomePATHNAME2ID toTable useMart * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented code objects: ‘queryKegg’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 getConceptTable 193.021 2.400 545.588 drawTable 183.545 2.896 523.636 groupReport 184.849 0.805 510.512 geneAnswersReadable 52.678 0.404 53.083 geneAnswersConceptNet 38.679 0.267 40.986 geneAnswersConceptRelation 38.338 0.352 42.009 geneAnswersBuilder 34.204 0.475 38.679 GeneAnswers-class 29.681 1.360 31.041 GeneAnswers-package 29.854 0.526 30.380 getConnectedGraph 28.327 0.332 28.660 buildNet 27.311 0.532 27.844 geneAnswersHeatmap 27.210 0.220 27.431 geneAnswersHomoMapping 27.102 0.200 27.304 geneAnswersConcepts 26.570 0.232 27.591 getMultiLayerGraphIDs 26.275 0.240 26.515 geneAnswersChartPlots 25.341 0.116 25.458 geneAnswersSort 24.769 0.140 24.909 getGOList 15.047 0.345 15.509 getPATHList 3.766 0.008 10.559 * 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 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.14-bioc/meat/GeneAnswers.Rcheck/00check.log’ for details.