############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.12.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (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 visualizeSegments 84.244 2.635 88.136 cnSegmentation 82.960 3.445 87.458 DMR 46.795 0.734 49.034 bSubMostVariable 38.915 0.487 39.689 testEnrichment 36.664 1.700 40.178 compareMouseTissueReference 28.937 0.532 30.093 compareMouseStrainReference 25.685 0.340 27.484 diffRefSet 23.631 0.386 24.553 testEnrichmentGene 23.043 0.942 25.017 visualizeGene 18.587 0.444 20.099 createUCSCtrack 18.564 0.228 19.402 DML 17.419 0.978 19.529 deidentify 17.430 0.346 18.350 getProbesByChromosome 17.020 0.199 17.584 print.sesameQC 15.819 1.207 17.354 bSubProbes 16.655 0.332 17.512 reIdentify 16.107 0.633 17.502 sdf_read_table 15.943 0.671 17.177 attachManifest 15.979 0.354 16.970 print.DMLSummary 16.081 0.139 16.907 getProbesByGene 15.923 0.187 16.743 as.data.frame.sesameQC 14.545 1.182 16.002 getRefSet 14.862 0.121 15.238 dmContrasts 14.593 0.290 15.188 summaryExtractTest 14.496 0.146 15.178 getDatabaseSetOverlap 14.341 0.284 15.507 bisConversionControl 14.195 0.265 15.488 calcDatabaseSetStatisticsAll 13.442 0.713 16.286 inferTissue 13.533 0.426 15.710 estimateLeukocyte 13.416 0.407 14.349 sesameQC 12.088 1.203 13.571 inferStrain 12.876 0.408 14.269 inferSex 12.008 0.321 12.958 dyeBiasCorrMostBalanced 11.476 0.302 12.408 SNPcheck 11.263 0.369 12.313 getProbesByRegion 8.809 0.099 9.176 setMaskBySpecies 8.609 0.152 9.351 qualityMask 8.316 0.231 9.245 getNormCtls 8.293 0.167 9.116 getAutosomeProbes 8.239 0.097 8.592 qualityRank 8.123 0.158 9.185 dyeBiasCorr 6.613 0.185 7.549 totalIntensities 6.465 0.197 7.286 controls 6.131 0.168 7.007 probeSuccessRate 6.049 0.238 6.862 bSubComplete 6.158 0.111 6.544 SigDF 6.075 0.142 6.883 getSexInfo 5.119 0.231 5.737 predictMouseAgeInMonth 5.172 0.153 7.107 getAFTypeIbySumAlleles 5.155 0.159 5.840 setMask 5.027 0.205 5.496 sdf_write_table 4.971 0.212 5.565 dyeBiasCorrTypeINorm 4.739 0.327 5.342 createDatabaseSetNetwork 4.866 0.076 5.204 predictAgeHorvath353 4.829 0.096 5.336 compareDatbaseSetOverlap 4.656 0.099 5.014 formatVCF 3.057 0.082 5.280 * 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