############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings sesame_1.14.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck' * using R version 4.2.1 (2022-06-23 ucrt) * using platform: x86_64-w64-mingw32 (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 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_plotHeatSNPs 39.16 1.13 40.38 DMR 35.57 0.64 36.42 sesameQC_calcStats 34.33 0.93 35.28 KYCG_plotEnrichAll 28.71 1.35 37.15 DML 25.78 1.77 28.99 inferSpecies 23.90 0.76 31.71 dyeBiasCorrMostBalanced 22.34 0.51 33.82 matchDesign 19.34 0.39 19.79 sesameQC_plotBetaByDesign 18.61 0.59 19.20 KYCG_plotMeta 16.90 0.70 22.03 sesameQC_plotBar 16.92 0.42 26.66 visualizeGene 15.29 0.59 16.11 probeSuccessRate 14.97 0.77 15.84 KYCG_plotMetaEnrichment 14.30 0.52 14.87 compareMouseStrainReference 14.11 0.71 16.50 KYCG_annoProbes 14.14 0.56 15.75 getSexInfo 14.02 0.57 14.70 diffRefSet 13.88 0.54 22.83 getRefSet 12.42 0.52 13.11 compareMouseTissueReference 12.36 0.57 13.10 prepSesame 12.25 0.58 12.89 KYCG_buildGeneDBs 12.37 0.39 19.45 inferStrain 11.99 0.63 12.62 sdf_read_table 12.06 0.30 12.39 testEnrichmentGSEA 11.57 0.61 13.01 dyeBiasCorr 11.19 0.49 11.87 dbStats 10.58 0.54 18.43 testEnrichment 9.97 0.66 10.69 detectionIB 9.43 0.56 10.02 controls 9.23 0.65 10.08 sdf_write_table 8.94 0.27 9.22 mapToMammal40 8.33 0.49 9.02 formatVCF 8.26 0.32 9.87 openSesame 8.13 0.45 9.34 estimateLeukocyte 7.83 0.33 13.85 inferTissue 7.59 0.42 8.17 inferSex 7.57 0.34 8.10 createUCSCtrack 7.44 0.46 9.96 detectionPnegEcdf 6.94 0.39 7.39 scrubSoft 7.06 0.22 7.28 dyeBiasNL 6.99 0.28 7.29 bisConversionControl 6.78 0.37 10.67 print.DMLSummary 6.24 0.20 6.47 sesameQC_rankStats 5.93 0.36 6.36 noMasked 5.80 0.28 6.11 predictAgeHorvath353 5.73 0.32 6.11 deidentify 5.58 0.44 6.12 scrub 5.58 0.26 5.84 summaryExtractTest 5.51 0.23 5.77 inferSexKaryotypes 5.54 0.10 5.76 openSesameToFile 5.18 0.27 5.46 predictAgeSkinBlood 5.05 0.28 5.48 reIdentify 5.13 0.15 5.32 sesameQC_getStats 5.09 0.07 5.15 predictMouseAgeInMonth 4.66 0.45 5.14 updateSigDF 4.14 0.27 6.20 checkLevels 3.58 0.25 6.27 * 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