############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings sesame_1.12.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.12.9’ * package encoding: UTF-8 * 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 ‘sesame’ 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 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 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 ... 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cnSegmentation 48.559 2.263 51.509 visualizeSegments 48.646 1.919 51.397 DMR 32.709 1.721 35.372 testEnrichment 26.260 1.636 28.923 bSubMostVariable 20.945 0.929 22.125 testEnrichmentGene 15.358 1.092 17.208 diffRefSet 14.997 0.875 16.203 compareMouseTissueReference 14.674 1.004 16.099 compareMouseStrainReference 14.011 0.617 15.919 print.DMLSummary 12.095 1.068 13.577 visualizeGene 11.917 0.888 13.691 getProbesByChromosome 11.896 0.656 12.805 DML 11.052 1.239 12.870 createUCSCtrack 11.202 0.652 12.286 getProbesByGene 11.001 0.816 12.247 as.data.frame.sesameQC 10.649 0.744 11.780 bSubProbes 10.694 0.623 11.650 attachManifest 10.572 0.672 11.571 sdf_read_table 10.498 0.612 11.623 bisConversionControl 10.289 0.768 11.647 sesameQC 9.891 1.032 11.088 inferTissue 9.781 0.789 12.196 calcDatabaseSetStatisticsAll 9.577 0.954 19.695 getRefSet 9.965 0.539 10.668 print.sesameQC 9.384 1.084 10.721 getDatabaseSetOverlap 9.407 0.744 10.692 deidentify 9.210 0.713 10.427 dyeBiasCorrMostBalanced 8.878 0.600 9.904 reIdentify 8.713 0.659 9.893 estimateLeukocyte 8.675 0.508 9.704 inferStrain 8.242 0.797 9.632 dmContrasts 8.444 0.540 9.359 summaryExtractTest 7.905 0.536 8.813 SNPcheck 7.712 0.523 8.750 getProbesByRegion 6.712 0.619 7.497 bSubComplete 6.395 0.604 7.269 qualityRank 6.069 0.648 7.407 inferSex 5.896 0.485 6.730 setMaskBySpecies 5.679 0.444 6.646 getNormCtls 5.548 0.569 6.639 qualityMask 5.329 0.386 6.222 getSexInfo 4.956 0.681 5.802 dyeBiasCorrTypeINorm 4.742 0.536 5.442 getAutosomeProbes 4.763 0.256 5.274 SigDF 4.521 0.400 5.257 dyeBiasCorr 4.499 0.332 5.372 probeSuccessRate 4.477 0.303 5.288 predictMouseAgeInMonth 4.045 0.443 7.049 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK