############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FGNet_3.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/FGNet.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FGNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FGNet’ version ‘3.26.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘FGNet’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE buildGeneSets: no visible global function definition for ‘columns’ buildGeneSets: no visible binding for global variable ‘GO.db’ buildGeneSets: no visible binding for global variable ‘reactomePATHID2NAME’ fea_gage: no visible global function definition for ‘exprs’ fea_gage: no visible global function definition for ‘gage’ fea_gage: no visible global function definition for ‘esset.grp’ fea_gtLinker_getResults: no visible global function definition for ‘url.exists’ fea_topGO: no visible global function definition for ‘groupGOTerms’ fea_topGO: no visible binding for global variable ‘annFUN.gene2GO’ fea_topGO: no visible global function definition for ‘getSigGroups’ fea_topGO: no visible global function definition for ‘GenTable’ fea_topGO : : no visible global function definition for ‘genesInTerm’ fea_topGO : : no visible global function definition for ‘sigGenes’ formatResultsFile: no visible binding for global variable ‘rawResults’ format_david: no visible global function definition for ‘getURL’ plotGoAncestors : : no visible binding for global variable ‘GOTERM’ processFile: no visible binding for '<<-' assignment to ‘rawResults’ processFile: no visible binding for global variable ‘rawResults’ refList: no visible global function definition for ‘columns’ submitQuery: no visible global function definition for ‘readList’ tabFEA_fill: no visible binding for global variable ‘GtkShadowType’ tabFEA_fill: no visible global function definition for ‘gtkVBox’ tabFEA_fill: no visible global function definition for ‘pangoFontDescriptionFromString’ tabFEA_fill: no visible global function definition for ‘gtkFrameSetShadowType’ tabFEA_fill: no visible global function definition for ‘gtkEntryNew’ tabFEA_fill: no visible global function definition for ‘newDavidVars’ tabFEA_fill: no visible global function definition for ‘tabDavid_fill’ tabFEA_fill: no visible binding for '<<-' assignment to ‘rawResults’ tabFEA_fill: no visible global function definition for ‘gtkLabelNew’ tabGTL_fill: no visible binding for global variable ‘GtkShadowType’ tabGage_fill: no visible binding for global variable ‘GtkShadowType’ tabHelp_fill: no visible binding for global variable ‘GtkShadowType’ tabNetwork_common_fill: no visible binding for global variable ‘GtkShadowType’ tabNetwork_common_fill: no visible global function definition for ‘pangoFontDescriptionFromString’ tabNetwork_common_fill: no visible global function definition for ‘gSignalConnect’ tabNetwork_fill: no visible global function definition for ‘gtkLabelNew’ tabOther_fill: no visible binding for global variable ‘GtkShadowType’ tabOther_fill : : no visible binding for global variable ‘GtkShadowType’ tabPlotNetwork_fill: no visible binding for global variable ‘GtkShadowType’ tabSubNetwork_fill: no visible binding for global variable ‘GtkShadowType’ tabTopGo_fill: no visible binding for global variable ‘GtkShadowType’ tabTopGo_fill: no visible binding for global variable ‘evidenceScroll’ viewFile: no visible binding for global variable ‘rawResults’ Undefined global functions or variables: GO.db GOTERM GenTable GtkShadowType annFUN.gene2GO columns esset.grp evidenceScroll exprs gSignalConnect gage genesInTerm getSigGroups getURL groupGOTerms gtkEntryNew gtkFrameSetShadowType gtkLabelNew gtkVBox newDavidVars pangoFontDescriptionFromString rawResults reactomePATHID2NAME readList sigGenes tabDavid_fill url.exists * 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 plotGoAncestors 8.43 0.62 9.058 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * 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 ‘/Users/biocbuild/bbs-3.13-bioc/meat/FGNet.Rcheck/00check.log’ for details.