############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings topGO_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/topGO.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘topGO/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘topGO’ version ‘2.54.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi', 'SparseM' 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 ‘topGO’ 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE 'library' or 'require' calls in package code: ‘Rgraphviz’ ‘multtest’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing object imported by a ':::' call: ‘globaltest:::globaltest’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GOplot: no visible global function definition for ‘getDefaultAttrs’ GOplot: no visible global function definition for ‘agopen’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘getNodeCenter’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘pieGlyph’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘getX’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘getY’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘getNodeLW’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘drawTxtLabel’ GOplot.counts : plotSigChart : buildDrawing : : no visible global function definition for ‘txtLabel’ GOplot.counts : plotSigChart: no visible global function definition for ‘AgNode’ GOplot.counts : plotSigChart : : no visible global function definition for ‘name’ GOplot.counts : plotSigChart : : no visible global function definition for ‘getNodeCenter’ GOplot.counts : plotSigChart: no visible global function definition for ‘getNodeXY’ GOplot.counts : plotSigChart: no visible global function definition for ‘getY’ GOplot.counts: no visible global function definition for ‘getDefaultAttrs’ GOplot.counts: no visible global function definition for ‘agopen’ getPvalues: no visible global function definition for ‘mt.teststat’ getPvalues: no visible global function definition for ‘mt.rawp2adjp’ printDOT: no visible global function definition for ‘getDefaultAttrs’ printDOT: no visible global function definition for ‘toDot’ GOSumTest,classicScore: no visible binding for global variable ‘.PERMSUM.MAT’ GOSumTest,classicScore: no visible binding for global variable ‘.PERMSUM.LOOKUP’ initialize,classicExpr: no visible global function definition for ‘error’ scoresInTerm,topGOdata-missing: no visible global function definition for ‘scoreInNode’ Undefined global functions or variables: .PERMSUM.LOOKUP .PERMSUM.MAT AgNode agopen drawTxtLabel error getDefaultAttrs getNodeCenter getNodeLW getNodeXY getX getY mt.rawp2adjp mt.teststat name pieGlyph scoreInNode toDot txtLabel * 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘topGO.Rnw’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/topGO.Rcheck/00check.log’ for details.