############################################################################## ############################################################################## ### ### 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 50.384 3.319 54.850 imputeBetasByGenomicNeighbors 40.521 1.546 42.501 inferSex 28.831 1.382 30.499 KYCG_plotMeta 27.159 1.129 28.715 sesameQC_calcStats 25.867 2.127 28.277 sesameQC_plotHeatSNPs 23.126 2.045 25.572 imputeBetas 21.791 1.636 23.770 KYCG_plotEnrichAll 21.384 1.119 23.185 ELBAR 18.083 3.157 21.577 KYCG_annoProbes 15.762 0.974 17.342 diffRefSet 15.921 0.711 16.880 inferSpecies 14.627 0.779 15.712 sesameQC_plotBar 14.506 0.398 15.360 compareMouseStrainReference 14.090 0.553 14.856 getRefSet 13.919 0.544 14.911 KYCG_plotMetaEnrichment 13.482 0.616 14.470 visualizeGene 12.220 0.808 13.815 testEnrichmentSEA 11.766 1.181 13.191 compareReference 12.348 0.506 13.057 sesameQC_plotBetaByDesign 11.491 1.332 12.978 KYCG_buildGeneDBs 11.982 0.507 12.695 matchDesign 11.644 0.725 12.561 DML 9.653 1.278 11.177 sdf_read_table 10.235 0.505 11.025 DMR 10.108 0.314 10.658 estimateLeukocyte 8.855 0.624 9.673 inferStrain 8.763 0.644 9.599 inferTissue 7.749 1.484 9.437 getMask 7.964 0.556 8.793 dbStats 7.226 0.747 8.174 createUCSCtrack 7.090 0.384 7.641 testEnrichment 6.554 0.845 7.801 probeSuccessRate 6.552 0.515 7.919 KYCG_plotSetEnrichment 6.511 0.484 7.203 dyeBiasCorrMostBalanced 6.619 0.276 7.048 deidentify 6.404 0.325 6.880 openSesame 5.768 0.691 6.668 dyeBiasNL 5.894 0.552 6.552 bisConversionControl 5.436 0.245 5.824 reIdentify 5.383 0.240 5.788 scrubSoft 3.910 1.254 5.267 prepSesame 4.549 0.448 5.129 sesameQC_rankStats 4.299 0.548 5.024 * 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