############################################################################## ############################################################################## ### ### 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_1.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.22.1’ * 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 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 127.567 6.554 137.401 imputeBetasByGenomicNeighbors 37.748 1.472 39.510 sesameQC_calcStats 24.963 2.197 27.326 inferSex 25.428 1.467 27.134 KYCG_plotMeta 24.244 0.904 25.346 sesameQC_plotHeatSNPs 21.617 2.094 23.907 imputeBetas 20.206 1.535 21.977 KYCG_plotEnrichAll 20.515 1.151 22.110 ELBAR 16.441 3.008 19.653 inferSpecies 15.369 0.787 16.599 KYCG_annoProbes 14.592 0.871 15.668 sesameQC_plotBar 14.351 0.363 14.941 diffRefSet 13.938 0.593 14.661 sesameQC_plotBetaByDesign 12.248 2.019 14.396 KYCG_plotMetaEnrichment 13.155 0.577 14.160 matchDesign 12.850 0.664 13.628 testEnrichmentSEA 12.485 0.897 13.600 getRefSet 12.531 0.592 13.298 compareMouseStrainReference 11.963 0.480 12.577 visualizeGene 11.545 0.628 12.426 sdf_read_table 10.562 1.360 12.194 compareReference 11.328 0.482 11.940 inferStrain 10.876 0.577 11.839 KYCG_buildGeneDBs 10.945 0.456 11.536 inferTissue 8.290 2.132 10.617 DML 9.162 1.191 10.669 DMR 8.949 0.266 9.340 estimateLeukocyte 8.562 0.597 9.433 getMask 7.453 0.668 8.373 openSesame 6.868 1.057 8.139 dbStats 7.228 0.642 7.989 testEnrichment 6.746 1.038 8.118 probeSuccessRate 6.579 0.503 7.407 createUCSCtrack 6.477 0.346 6.938 dyeBiasCorrMostBalanced 6.316 0.232 6.907 KYCG_plotSetEnrichment 5.814 0.490 6.575 deidentify 5.965 0.336 6.775 dyeBiasNL 5.516 0.532 6.113 reIdentify 5.487 0.272 5.950 prepSesame 4.862 0.537 5.486 bisConversionControl 5.090 0.260 5.461 * 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