############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:limma.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings limma_3.63.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/limma.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * 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 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘limma/DESCRIPTION’ ... OK * this is package ‘limma’ version ‘3.63.3’ * 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 ‘limma’ can be installed ... OK * used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * 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 ... 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Non-topic package-anchored link(s) in Rd file '02classes.Rd': ‘[limma:rglist]{RGList}’ ‘[limma:malist]{MAList}’ ‘[limma:EList]{EListRaw}’ ‘[limma:EList]{EList}’ ‘[limma:marraylm]{MArrayLM}’ ‘[limma:TestResults]{TestResults}’ ‘[limma:asdataframe]{as.data.frame}’ ‘[limma:LargeDataObject]{LargeDataObject}’ Non-topic package-anchored link(s) in Rd file '03reading.Rd': ‘[limma:merge]{merge}’ Non-topic package-anchored link(s) in Rd file '06linearmodels.Rd': ‘[limma:marraylm]{MArrayLM}’ Non-topic package-anchored link(s) in Rd file '08Tests.Rd': ‘[limma:TestResults]{TestResults}’ Non-topic package-anchored link(s) in Rd file '09Diagnostics.Rd': ‘[limma:anova-method]{anova}’ Non-topic package-anchored link(s) in Rd file 'EList.Rd': ‘[limma:dim]{dim}’ ‘[limma:LargeDataObject]{LargeDataObject}’ ‘[Biobase:class.ExpressionSet]{ExpressionSet}’ Non-topic package-anchored link(s) in Rd file 'backgroundcorrect.Rd': ‘[limma:EList]{EListRaw}’ ‘[limma:rglist]{RGList}’ Non-topic package-anchored link(s) in Rd file 'bwss.matrix.Rd': ‘[limma:anova-method]{anova}’ Non-topic package-anchored link(s) in Rd file 'cbind.Rd': ‘[limma:rglist]{RGList}’ ‘[limma:malist]{MAList}’ ‘[limma:EList]{EList}’ ‘[limma:EList]{EListRaw}’ Non-topic package-anchored link(s) in Rd file 'contrasts.fit.Rd': ‘[limma:marraylm]{MArrayLM}’ Non-topic package-anchored link(s) in Rd file 'dupcor.Rd': ‘[statmod:mixedmodel]{mixedModel2Fit}’ Non-topic package-anchored link(s) in Rd file 'intraspotCorrelation.Rd': ‘[limma:malist]{MAList}’ ‘[statmod:remlscor]{remlscore}’ Non-topic package-anchored link(s) in Rd file 'lm.series.Rd': ‘[stats:lmfit]{lm.fit}’ Non-topic package-anchored link(s) in Rd file 'lmFit.Rd': ‘[limma:marraylm]{MArrayLM}’ Non-topic package-anchored link(s) in Rd file 'lmscFit.Rd': ‘[limma:malist]{MAList}’ ‘[limma:marraylm]{MArrayLM}’ ‘[stats:lmfit]{lm.fit}’ Non-topic package-anchored link(s) in Rd file 'malist.Rd': ‘[limma:PrintLayout]{PrintLayout}’ ‘[limma:dim]{dim}’ ‘[limma:LargeDataObject]{LargeDataObject}’ Non-topic package-anchored link(s) in Rd file 'marraylm.Rd': ‘[limma:dim]{dim}’ Non-topic package-anchored link(s) in Rd file 'merge.Rd': ‘[limma:rglist]{RGList}’ ‘[limma:malist]{MAList}’ ‘[limma:EList]{EList}’ ‘[limma:EList]{EListRaw}’ Non-topic package-anchored link(s) in Rd file 'normalizeVSN.Rd': ‘[limma:rglist]{RGList}’ ‘[limma:malist]{MAList}’ Non-topic package-anchored link(s) in Rd file 'normalizeWithinArrays.Rd': ‘[limma:PrintLayout]{PrintLayout-class}’ ‘[limma:malist]{MAList}’ Non-topic package-anchored link(s) in Rd file 'normalizebetweenarrays.Rd': ‘[limma:EList]{EListRaw}’ ‘[limma:rglist]{RGList}’ ‘[limma:malist]{MAList}’ ‘[affy:normalize-methods]{normalize-methods}’ Non-topic package-anchored link(s) in Rd file 'plotma3by2.Rd': ‘[limma:plotma]{plotMA}’ Non-topic package-anchored link(s) in Rd file 'printtipWeights.Rd': ‘[limma:PrintLayout]{PrintLayout-class}’ Non-topic package-anchored link(s) in Rd file 'read.maimages.Rd': ‘[limma:EList]{EListRaw}’ ‘[limma:rglist]{RGList}’ Non-topic package-anchored link(s) in Rd file 'rglist.Rd': ‘[limma:PrintLayout]{PrintLayout}’ ‘[limma:merge]{merged}’ ‘[limma:dim]{dim}’ ‘[limma:LargeDataObject]{LargeDataObject}’ Non-topic package-anchored link(s) in Rd file 'voom.Rd': ‘[limma:EList]{EList}’ Non-topic package-anchored link(s) in Rd file 'voomWithQualityWeights.Rd': ‘[limma:EList]{EList}’ 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 line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * 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 alias2Symbol 4.782 0.308 5.095 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘limma-Tests.R’ Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ... OK 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 * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/limma.Rcheck/00check.log’ for details.