############################################################################## ############################################################################## ### ### 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_1.22.0.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 ‘1.22.0’ * 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 126.027 5.800 134.483 inferSex 40.540 1.970 43.144 sesameQC_calcStats 25.319 2.355 28.006 KYCG_plotMeta 25.427 1.124 26.999 sesameQC_plotHeatSNPs 21.130 1.797 23.228 KYCG_plotEnrichAll 20.886 1.146 23.145 ELBAR 17.413 3.186 20.957 inferSpecies 15.828 0.749 16.891 KYCG_annoProbes 15.374 0.927 16.659 diffRefSet 15.400 0.773 16.460 KYCG_plotMetaEnrichment 14.439 0.672 15.614 sesameQC_plotBar 14.287 0.607 15.373 compareMouseStrainReference 13.709 0.462 14.398 getRefSet 12.886 0.574 13.712 sesameQC_plotBetaByDesign 11.944 1.361 13.432 compareReference 12.089 0.593 12.947 KYCG_buildGeneDBs 11.749 0.520 12.489 testEnrichmentSEA 11.272 0.941 12.679 matchDesign 11.519 0.673 12.370 visualizeGene 11.551 0.556 12.370 DML 9.603 1.376 11.220 DMR 9.988 0.359 10.560 sdf_read_table 9.446 0.512 10.262 inferStrain 8.587 0.706 9.754 inferTissue 7.773 1.519 9.490 dbStats 8.463 0.735 9.420 dyeBiasNL 8.055 0.650 8.829 estimateLeukocyte 7.426 0.558 8.182 KYCG_plotSetEnrichment 6.803 0.537 7.505 createUCSCtrack 6.795 0.415 7.388 testEnrichment 6.358 0.827 7.413 dyeBiasCorrMostBalanced 6.535 0.324 7.022 deidentify 6.441 0.405 7.038 probeSuccessRate 6.304 0.483 7.062 openSesame 5.779 0.710 6.686 getMask 5.772 0.475 6.507 bisConversionControl 5.306 0.276 5.750 reIdentify 4.997 0.248 5.619 prepSesame 4.364 0.550 5.016 listAvailableMasks 2.025 0.179 5.473 * 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