################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:topGO.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings topGO_2.62.0.tar.gz###############################################################################################################################################################* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/topGO.Rcheck’* using R version 4.5.2 (2025-10-31)* using platform: x86_64-pc-linux-gnu* R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0* running under: Ubuntu 24.04.3 LTS* using session charset: UTF-8* checking for file ‘topGO/DESCRIPTION’ ... OK* checking extension type ... Package* this is package ‘topGO’ version ‘2.62.0’* package encoding: UTF-8* checking package namespace information ... OK* checking package dependencies ... INFODepends: includes the non-default packages: 'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi', 'SparseM'Adding so many packages to the search path is excessive and importingselectively 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 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 ... OK* checking whether the namespace can be unloaded cleanly ... OK* checking loading without being on the library search path ... OK* checking whether startup messages can be suppressed ... NOTEgroupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.It looks like this package (or a package it requires) has a startupmessage 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 ... WARNINGFound a .Internal call in methods for the following S4 generic: ‘GOSumTest’Packages should not call .Internal(): it is not part of the API, foruse only by R itself and subject to change without notice.In addition to the above warning(s), found the following notes:GOplot: no visible global function definition for ‘getDefaultAttrs’GOplot: no visible global function definition for ‘agopen’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getNodeCenter’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘pieGlyph’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getX’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getY’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘getNodeLW’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘drawTxtLabel’GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible global function definition for ‘txtLabel’GOplot.counts : plotSigChart: no visible global function definition for ‘AgNode’GOplot.counts : plotSigChart : <anonymous>: no visible global function definition for ‘name’GOplot.counts : plotSigChart : <anonymous>: 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 ... OK* checking re-building of vignette outputs ... OK* checking PDF version of manual ... OK* DONEStatus: 1 WARNING, 2 NOTEsSee ‘/home/biocbuild/bbs-3.22-bioc/meat/topGO.Rcheck/00check.log’for details.
################################################################################################################################################################## Running command:###### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL topGO###############################################################################################################################################################* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’* installing *source* package ‘topGO’ ...** this is package ‘topGO’ version ‘2.62.0’** using staged installation** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary locationgroupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.** testing if installed package can be loaded from final locationgroupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.** testing if installed package keeps a record of temporary installation path* DONE (topGO)
