############################################################################## ############################################################################## ### ### 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_1.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck’ * using R version 4.2.1 (2022-06-23) * 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 ‘1.14.2’ * 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 sesameQC_calcStats 56.757 2.370 59.478 sesameQC_plotHeatSNPs 46.912 1.824 48.998 DMR 46.019 0.617 47.830 KYCG_plotEnrichAll 37.844 0.903 40.580 inferSpecies 33.888 0.847 35.626 DML 33.695 0.836 35.098 dyeBiasCorrMostBalanced 27.956 0.462 29.054 sesameQC_plotBetaByDesign 25.666 1.360 27.065 compareMouseStrainReference 26.144 0.317 26.861 sesameQC_plotBar 24.361 0.602 25.337 KYCG_plotMeta 23.570 0.657 25.019 matchDesign 23.248 0.704 24.302 compareMouseTissueReference 23.057 0.421 23.983 diffRefSet 22.337 0.661 23.613 getSexInfo 20.566 0.504 21.949 detectionIB 18.862 1.758 20.821 KYCG_annoProbes 19.192 0.694 20.616 probeSuccessRate 19.171 0.479 20.941 KYCG_plotMetaEnrichment 18.885 0.498 20.301 inferStrain 18.469 0.692 19.616 getRefSet 17.663 0.430 18.578 prepSesame 17.352 0.679 18.843 dyeBiasCorr 16.507 0.467 17.839 KYCG_buildGeneDBs 15.675 0.434 16.554 visualizeGene 15.098 0.337 16.230 testEnrichmentGSEA 14.567 0.727 16.049 controls 14.272 0.435 15.541 testEnrichment 13.971 0.455 15.432 dbStats 12.098 0.731 13.391 inferTissue 11.792 0.731 12.973 deidentify 12.023 0.234 12.703 inferSex 11.266 0.357 12.160 detectionPnegEcdf 11.223 0.293 11.947 formatVCF 11.112 0.366 20.236 mapToMammal40 10.672 0.268 11.551 reIdentify 10.752 0.171 11.139 dyeBiasNL 10.478 0.400 11.147 openSesame 10.603 0.256 11.262 estimateLeukocyte 10.406 0.440 11.219 scrubSoft 10.092 0.710 10.811 sdf_read_table 10.139 0.409 10.741 noMasked 9.288 0.528 10.319 openSesameToFile 9.063 0.424 9.502 createUCSCtrack 8.894 0.221 9.593 scrub 8.509 0.425 8.950 inferSexKaryotypes 8.563 0.255 9.141 print.DMLSummary 7.969 0.374 8.936 bisConversionControl 7.800 0.179 8.317 predictAgeHorvath353 7.347 0.578 8.401 inferEthnicity 7.613 0.297 8.088 visualizeProbes 7.603 0.207 8.073 summaryExtractTest 7.122 0.572 8.242 noob 6.591 0.570 7.198 predictAgeSkinBlood 6.603 0.352 7.511 sesameQC_rankStats 6.181 0.455 7.200 sesameQC_getStats 6.371 0.242 6.630 qualityMask 6.109 0.193 6.528 KYCG_getDBs 5.745 0.216 6.444 predictMouseAgeInMonth 5.603 0.226 6.395 KYCG_plotPointRange 5.577 0.153 6.010 updateSigDF 5.187 0.229 5.912 sesameQC_plotIntensVsBetas 5.038 0.347 5.557 sesame-package 5.135 0.172 5.566 pOOBAH 4.910 0.288 5.203 checkLevels 4.855 0.230 5.260 totalIntensities 4.669 0.224 5.372 KYCG_plotWaterfall 4.737 0.138 5.193 meanIntensity 4.420 0.362 5.245 * 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