############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings sesame_1.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck’ * using R version 4.2.1 (2022-06-23) * 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 ‘1.14.2’ * 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 33.119 1.039 34.422 KYCG_plotEnrichAll 29.643 3.163 34.323 DMR 28.349 1.928 31.151 sesameQC_plotHeatSNPs 27.320 0.912 28.484 inferSpecies 21.652 2.044 24.447 DML 21.770 1.120 23.313 dyeBiasCorrMostBalanced 17.578 1.289 19.538 KYCG_plotMeta 17.115 1.260 18.959 sesameQC_plotBar 15.536 0.800 16.843 getSexInfo 14.852 1.024 16.717 matchDesign 14.812 0.887 15.910 sesameQC_plotBetaByDesign 14.646 0.455 15.100 probeSuccessRate 13.446 1.112 15.477 diffRefSet 13.295 1.060 14.699 KYCG_plotMetaEnrichment 12.934 1.137 14.760 KYCG_annoProbes 12.749 1.256 14.786 dyeBiasCorr 12.587 1.055 14.497 prepSesame 11.274 1.024 12.885 compareMouseTissueReference 11.459 0.836 12.625 KYCG_buildGeneDBs 10.752 1.164 12.248 compareMouseStrainReference 11.148 0.604 12.260 getRefSet 10.707 0.692 11.814 testEnrichment 10.221 0.975 12.120 inferStrain 10.064 0.868 11.452 visualizeGene 9.954 0.803 11.362 controls 9.795 0.829 11.370 dbStats 9.532 0.960 11.001 testEnrichmentGSEA 9.733 0.691 11.008 estimateLeukocyte 7.689 0.791 8.814 dyeBiasNL 7.911 0.456 8.530 inferSex 7.672 0.560 8.562 formatVCF 7.531 0.645 10.439 detectionIB 7.511 0.604 8.282 detectionPnegEcdf 7.316 0.588 8.335 inferTissue 7.174 0.696 8.199 mapToMammal40 6.726 0.576 8.064 openSesame 6.669 0.544 7.575 scrubSoft 6.352 0.319 6.671 reIdentify 6.004 0.628 6.797 noMasked 5.895 0.539 6.764 createUCSCtrack 5.895 0.460 6.771 sdf_read_table 5.878 0.321 6.450 predictAgeHorvath353 5.454 0.663 6.453 deidentify 5.445 0.428 6.384 sesame-package 5.359 0.476 5.999 bisConversionControl 5.282 0.532 6.145 print.DMLSummary 5.080 0.517 6.015 inferEthnicity 4.998 0.444 5.607 openSesameToFile 4.862 0.351 5.212 predictAgeSkinBlood 4.682 0.504 5.601 inferSexKaryotypes 4.650 0.353 5.170 summaryExtractTest 4.588 0.415 5.334 * 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