############################################################################## ############################################################################## ### ### 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_1.23.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.8’ * 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 code 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 whether startup messages can be suppressed ... 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 testEnrichmentGene 50.776 3.112 55.762 imputeBetasByGenomicNeighbors 40.084 1.563 42.117 inferSex 28.979 1.356 30.885 KYCG_plotMeta 26.642 1.036 28.049 sesameQC_calcStats 25.283 2.034 27.664 sesameQC_plotHeatSNPs 23.104 2.053 25.480 KYCG_plotEnrichAll 22.732 1.293 24.979 imputeBetas 22.090 1.640 24.101 ELBAR 18.104 3.204 21.648 KYCG_annoProbes 15.756 0.914 16.943 diffRefSet 15.314 0.680 16.212 inferSpecies 14.767 0.754 15.843 compareMouseStrainReference 14.655 0.561 15.426 sesameQC_plotBar 14.419 0.364 14.974 KYCG_plotMetaEnrichment 13.916 0.629 14.902 getRefSet 13.986 0.508 14.702 visualizeGene 12.937 0.873 14.276 sesameQC_plotBetaByDesign 12.090 1.455 13.698 testEnrichmentSEA 11.929 1.212 13.480 compareReference 12.094 0.532 12.952 matchDesign 11.840 0.698 12.806 KYCG_buildGeneDBs 11.872 0.505 12.596 sdf_read_table 10.414 0.537 11.271 DML 9.567 1.271 11.393 DMR 9.890 0.298 10.455 estimateLeukocyte 9.129 0.603 10.226 inferTissue 8.033 1.437 9.688 inferStrain 8.605 0.650 9.436 getMask 8.094 0.677 9.225 dbStats 7.227 0.675 8.187 createUCSCtrack 7.065 0.367 7.706 testEnrichment 6.459 0.787 7.787 probeSuccessRate 6.584 0.564 7.491 dyeBiasCorrMostBalanced 6.648 0.265 7.101 KYCG_plotSetEnrichment 6.365 0.523 7.082 dyeBiasNL 6.214 0.548 6.874 deidentify 6.364 0.344 6.869 openSesame 5.908 0.632 6.844 bisConversionControl 5.620 0.304 6.358 reIdentify 5.420 0.205 5.964 scrubSoft 3.943 1.494 5.704 prepSesame 4.497 0.579 6.275 sesameQC_rankStats 4.414 0.512 5.085 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK