############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:eegc.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings eegc_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/eegc.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 ‘eegc/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘eegc’ version ‘1.28.0’ * 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 ‘eegc’ can be installed ... OK * checking installed package size ... NOTE installed size is 11.1Mb sub-directories of 1Mb or more: data 10.5Mb * 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 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 categorizeGene : : no visible global function definition for ‘quantile’ densityPlot: no visible binding for global variable ‘density’ densityPlot: no visible global function definition for ‘lines’ densityPlot: no visible global function definition for ‘axis’ densityPlot: no visible global function definition for ‘adjustcolor’ densityPlot: no visible global function definition for ‘legend’ densityPlot : : no visible global function definition for ‘quantile’ densityPlot: no visible global function definition for ‘text’ densityPlot: no visible global function definition for ‘dev.copy2pdf’ diffGene: no visible global function definition for ‘model.matrix’ diffGene: no visible binding for global variable ‘treat’ diffGene: no visible binding for global variable ‘control’ diffGene: no visible global function definition for ‘results’ diffGene: no visible global function definition for ‘p.adjust’ dotPercentage: no visible global function definition for ‘lines’ dotPercentage: no visible global function definition for ‘axis’ dotPercentage: no visible global function definition for ‘text’ dotPercentage: no visible global function definition for ‘par’ enrichment : enrichment : : no visible global function definition for ‘phyper’ enrichment : enrichment: no visible global function definition for ‘p.adjust’ functionEnrich: no visible global function definition for ‘is’ grnPlot: no visible global function definition for ‘title’ grnPlot: no visible global function definition for ‘legend’ markerScatter: no visible global function definition for ‘colorRampPalette’ markerScatter: no visible global function definition for ‘points’ markerScatter: no visible global function definition for ‘lm’ markerScatter: no visible global function definition for ‘abline’ markerScatter: no visible global function definition for ‘text’ markerScatter: no visible global function definition for ‘legend’ Undefined global functions or variables: abline adjustcolor axis colorRampPalette control density dev.copy2pdf is legend lines lm model.matrix p.adjust par phyper points quantile results text title treat Consider adding importFrom("grDevices", "adjustcolor", "colorRampPalette", "dev.copy2pdf") importFrom("graphics", "abline", "axis", "legend", "lines", "par", "points", "text", "title") importFrom("methods", "is") importFrom("stats", "density", "lm", "model.matrix", "p.adjust", "phyper", "quantile") 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 ... WARNING Missing link or links in documentation object 'barplotEnrich.Rd': ‘[DOSE]{barplot.enrichResult}’ See section 'Cross-references' in the 'Writing R Extensions' manual. * 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 LazyData ... WARNING LazyData DB of 10.5 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed functionEnrich 191.953 3.513 202.821 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘eegc.Rnw’... OK NONE * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘eegc.Rnw’ using knitr Quitting from lines 27-28 [style] (eegc.Rnw) Error: processing vignette 'eegc.Rnw' failed with diagnostics: there is no package called 'BiocStyle' --- failed re-building ‘eegc.Rnw’ SUMMARY: processing the following file failed: ‘eegc.Rnw’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 WARNINGs, 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/eegc.Rcheck/00check.log’ for details.