############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:limma.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings limma_3.66.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/limma.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘limma/DESCRIPTION’ ... OK * this is package ‘limma’ version ‘3.66.0’ * 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 ‘limma’ can be installed ... OK * used C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ * 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 6.167 0.311 6.522 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘limma-Tests.R’ Comparing ‘limma-Tests.Rout’ to ‘limma-Tests.Rout.save’ ...504,509c504,509 < Min. :-5.8801 Min. :-5.66985 < 1st Qu.:-1.1850 1st Qu.:-1.57014 < Median :-0.2164 Median : 0.04823 < Mean : 0.0349 Mean :-0.05481 < 3rd Qu.: 1.4964 3rd Qu.: 1.45113 < Max. : 7.0751 Max. : 6.19744 --- > Min. :-5.88010 Min. :-5.66985 > 1st Qu.:-1.18496 1st Qu.:-1.57014 > Median :-0.21642 Median : 0.04823 > Mean : 0.03489 Mean :-0.05481 > 3rd Qu.: 1.49638 3rd Qu.: 1.45113 > Max. : 7.07506 Max. : 6.19744 520c520 < [1,] -1.1669589 4.5558123 --- > [1,] -1.1669590 4.5558123 535c535 < [1,] -1.1669589 4.5558123 --- > [1,] -1.1669590 4.5558123 1236,1245c1236,1245 < GO:0070062 extracellular exosome CC 8 0 4 1.00000000 0.003047199 < GO:0065010 extracellular membrane-boun... CC 8 0 4 1.00000000 0.003047199 < GO:0043230 extracellular organelle CC 8 0 4 1.00000000 0.003047199 < GO:1903561 extracellular vesicle CC 8 0 4 1.00000000 0.003047199 < GO:0097190 apoptotic signaling pathway BP 3 3 0 0.01095238 1.000000000 < GO:0031252 cell leading edge CC 3 3 0 0.01095238 1.000000000 < GO:0032502 developmental process BP 26 6 6 0.59345898 0.018024293 < GO:0098609 cell-cell adhesion BP 6 4 0 0.02399362 1.000000000 < GO:0043009 chordate embryonic developm... BP 3 0 2 1.00000000 0.025788497 < GO:0072359 circulatory system developm... BP 3 0 2 1.00000000 0.025788497 --- > GO:0032502 developmental process BP 26 5 7 0.785697935 0.002720775 > GO:0070062 extracellular exosome CC 8 0 4 1.000000000 0.003047199 > GO:0065010 extracellular membrane-boun... CC 8 0 4 1.000000000 0.003047199 > GO:0043230 extracellular organelle CC 8 0 4 1.000000000 0.003047199 > GO:1903561 extracellular vesicle CC 8 0 4 1.000000000 0.003047199 > GO:0006915 apoptotic process BP 5 4 1 0.009503355 0.416247633 > GO:0008219 cell death BP 5 4 1 0.009503355 0.416247633 > GO:0012501 programmed cell death BP 5 4 1 0.009503355 0.416247633 > GO:0042981 regulation of apoptotic pro... BP 5 4 1 0.009503355 0.416247633 > GO:0043067 regulation of programmed ce... BP 5 4 1 0.009503355 0.416247633 1248,1257c1248,1257 < GO:0070062 extracellular exosome CC 8 0 4 1.000000 0.003047199 < GO:0065010 extracellular membrane-boun... CC 8 0 4 1.000000 0.003047199 < GO:0043230 extracellular organelle CC 8 0 4 1.000000 0.003047199 < GO:1903561 extracellular vesicle CC 8 0 4 1.000000 0.003047199 < GO:0032502 developmental process BP 26 6 6 0.593459 0.018024293 < GO:0043009 chordate embryonic developm... BP 3 0 2 1.000000 0.025788497 < GO:0072359 circulatory system developm... BP 3 0 2 1.000000 0.025788497 < GO:0009790 embryo development BP 3 0 2 1.000000 0.025788497 < GO:0009792 embryo development ending i... BP 3 0 2 1.000000 0.025788497 < GO:0007507 heart development BP 3 0 2 1.000000 0.025788497 --- > GO:0032502 developmental process BP 26 5 7 0.7856979 0.002720775 > GO:0070062 extracellular exosome CC 8 0 4 1.0000000 0.003047199 > GO:0065010 extracellular membrane-boun... CC 8 0 4 1.0000000 0.003047199 > GO:0043230 extracellular organelle CC 8 0 4 1.0000000 0.003047199 > GO:1903561 extracellular vesicle CC 8 0 4 1.0000000 0.003047199 > GO:0016485 protein processing BP 6 0 3 1.0000000 0.012551076 > GO:0043009 chordate embryonic developm... BP 3 0 2 1.0000000 0.025788497 > GO:0072359 circulatory system developm... BP 3 0 2 1.0000000 0.025788497 > GO:0009790 embryo development BP 3 0 2 1.0000000 0.025788497 > GO:0009792 embryo development ending i... BP 3 0 2 1.0000000 0.025788497 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/limma.Rcheck/00check.log’ for details.