############################################################################## ############################################################################## ### ### 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_1.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’ * using R version 4.2.3 (2023-03-15) * 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 ‘1.16.1’ * 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 KYCG_plotEnrichAll 23.692 0.838 25.134 sesameQC_calcStats 20.067 1.956 22.217 sesameQC_plotHeatSNPs 17.682 1.725 19.584 KYCG_plotMeta 14.809 0.674 15.744 inferSpecies 14.543 0.623 15.419 DMR 13.694 0.373 14.307 matchDesign 12.228 0.574 12.929 diffRefSet 11.013 0.431 11.601 sesameQC_plotBar 10.551 0.480 11.214 inferTissue 9.466 1.340 11.055 KYCG_annoProbes 10.209 0.458 11.130 sesameQC_plotBetaByDesign 9.699 0.935 10.655 KYCG_plotMetaEnrichment 9.960 0.478 10.670 compareMouseStrainReference 9.662 0.278 10.103 KYCG_buildGeneDBs 9.548 0.331 10.050 getRefSet 9.380 0.462 10.025 compareReference 9.197 0.522 9.919 testEnrichmentSEA 8.817 0.878 9.954 testEnrichment 8.904 0.729 9.944 detectionIB 8.351 1.103 9.588 visualizeGene 7.887 0.370 8.477 getSexInfo 7.706 0.422 8.359 sdf_read_table 7.519 0.445 8.117 DML 6.896 0.864 7.992 estimateLeukocyte 7.133 0.527 7.819 inferStrain 6.701 0.636 7.526 dbStats 6.608 0.697 7.484 dyeBiasNL 6.561 0.480 7.119 dyeBiasCorrMostBalanced 5.576 0.242 5.964 KYCG_plotSetEnrichment 4.976 0.548 5.700 probeSuccessRate 5.073 0.394 5.706 deidentify 4.963 0.274 5.427 createUCSCtrack 4.991 0.205 5.411 * 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