############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:limma.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings limma_3.65.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/limma.Rcheck’ * using R version 4.5.1 Patched (2025-06-14 r88325) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0 * running under: macOS Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘limma/DESCRIPTION’ ... OK * this is package ‘limma’ version ‘3.65.1’ * 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ * used SDK: ‘MacOSX11.3.sdk’ * 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 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 sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘limma-Tests.R’ Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...520c520 < [1,] -1.1669589 4.5558123 --- > [1,] -1.1669590 4.5558123 535c535 < [1,] -1.1669589 4.5558123 --- > [1,] -1.1669590 4.5558123 871,872c871,872 < mu+alpha 0.3333333 3.333333e-01 1.232595e-32 < mu+beta -0.3333333 1.232595e-32 3.333333e-01 --- > mu+alpha 0.3333333 3.333333e-01 1.110223e-16 > mu+beta -0.3333333 1.110223e-16 3.333333e-01 NOTE * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/limma.Rcheck/00check.log’ for details.