############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:sesame.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings sesame_1.12.9.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed visualizeSegments 56.11 0.57 57.38 cnSegmentation 51.99 2.77 60.02 DMR 42.79 1.07 47.83 testEnrichment 24.73 0.47 26.10 bSubMostVariable 22.52 0.61 23.28 sdf_read_table 19.44 0.47 20.23 compareMouseTissueReference 17.34 0.33 18.81 diffRefSet 16.05 0.31 17.13 testEnrichmentGene 15.90 0.36 16.82 DML 12.86 2.07 16.11 print.sesameQC 14.25 0.51 14.92 attachManifest 13.48 0.89 18.55 getProbesByChromosome 14.11 0.22 16.16 compareMouseStrainReference 13.99 0.07 14.91 as.data.frame.sesameQC 11.91 0.89 12.95 getProbesByGene 12.07 0.24 16.04 visualizeGene 12.05 0.26 12.80 createUCSCtrack 12.02 0.20 12.58 bisConversionControl 11.30 0.37 13.62 getRefSet 11.47 0.16 11.76 dyeBiasCorrMostBalanced 11.43 0.18 18.42 sdf_write_table 11.25 0.28 11.82 calcDatabaseSetStatisticsAll 10.13 1.36 13.33 getDatabaseSetOverlap 11.03 0.25 11.87 estimateLeukocyte 10.94 0.29 13.92 SNPcheck 9.97 0.81 53.70 deidentify 10.23 0.18 11.06 bSubProbes 9.85 0.46 10.66 inferTissue 9.67 0.63 11.37 print.DMLSummary 9.86 0.16 10.34 summaryExtractTest 9.61 0.17 10.12 sesameQC 9.15 0.49 9.81 inferStrain 8.94 0.53 10.82 dmContrasts 9.33 0.10 9.59 reIdentify 8.79 0.33 9.44 inferSex 7.55 0.36 8.27 setMaskBySpecies 7.39 0.28 8.17 qualityRank 6.21 0.22 6.96 qualityMask 5.94 0.18 6.85 getNormCtls 5.73 0.19 6.41 dyeBiasCorrTypeINorm 5.72 0.10 5.97 bSubComplete 5.30 0.28 9.81 SigDF 5.15 0.30 9.67 dyeBiasCorr 5.21 0.19 5.69 getAutosomeProbes 5.12 0.10 5.37 getProbesByRegion 4.89 0.06 5.11 totalIntensities 4.64 0.17 5.12 probeSuccessRate 4.55 0.10 5.14 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed visualizeSegments 55.73 0.83 57.27 cnSegmentation 50.85 1.27 52.61 DMR 33.49 0.87 35.30 testEnrichment 25.89 1.03 27.78 bSubMostVariable 22.51 0.25 22.92 compareMouseTissueReference 17.80 0.22 18.39 diffRefSet 15.69 0.39 16.72 sdf_read_table 15.58 0.31 16.28 testEnrichmentGene 15.18 0.37 16.15 compareMouseStrainReference 14.53 0.14 15.47 visualizeGene 13.25 0.39 14.13 as.data.frame.sesameQC 12.28 1.07 13.53 DML 11.90 0.92 13.30 createUCSCtrack 11.98 0.28 12.58 getProbesByChromosome 11.50 0.19 11.86 calcDatabaseSetStatisticsAll 11.18 0.39 13.61 getDatabaseSetOverlap 11.04 0.39 11.97 print.sesameQC 10.28 0.98 11.44 bSubProbes 10.53 0.34 11.22 bisConversionControl 10.46 0.28 11.22 print.DMLSummary 10.41 0.22 10.91 inferTissue 10.04 0.44 11.62 attachManifest 10.13 0.33 10.81 getProbesByGene 10.05 0.26 10.65 deidentify 9.87 0.19 10.43 sdf_write_table 9.85 0.16 10.19 inferStrain 9.44 0.56 10.50 sesameQC 9.09 0.81 10.08 estimateLeukocyte 9.59 0.25 10.19 dmContrasts 9.65 0.17 10.01 getRefSet 9.59 0.14 9.94 reIdentify 9.42 0.24 9.99 summaryExtractTest 9.47 0.18 9.96 SNPcheck 8.09 0.22 8.64 dyeBiasCorrMostBalanced 8.03 0.17 8.84 getNormCtls 7.44 0.27 8.00 inferSex 6.58 0.50 7.39 qualityRank 6.84 0.19 7.51 getProbesByRegion 6.70 0.14 7.00 setMaskBySpecies 6.50 0.17 6.98 qualityMask 5.55 0.21 6.10 bSubComplete 5.42 0.10 5.67 getSexInfo 5.10 0.27 5.53 SigDF 5.11 0.22 5.66 totalIntensities 5.16 0.14 5.62 dyeBiasCorr 4.94 0.22 5.82 getAutosomeProbes 5.00 0.10 5.25 probeSuccessRate 4.67 0.24 5.25 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'testthat.R' OK ** running tests for arch 'x64' ... 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