############################################################################## ############################################################################## ### ### 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.24.0’ * 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 67.361 3.324 71.245 imputeBetasByGenomicNeighbors 42.083 1.135 43.385 inferSex 28.986 0.960 30.149 sesameQC_calcStats 25.261 1.689 27.153 KYCG_plotMeta 25.588 1.043 26.772 KYCG_plotEnrichAll 24.804 1.050 26.108 sesameQC_plotHeatSNPs 22.614 1.217 23.941 imputeBetas 21.900 1.500 23.542 sesameQC_plotBar 20.455 0.364 21.010 ELBAR 17.362 2.710 20.214 diffRefSet 17.204 0.635 18.036 inferSpecies 17.126 0.689 17.871 KYCG_annoProbes 16.958 0.641 17.708 KYCG_plotMetaEnrichment 16.226 0.618 17.157 getRefSet 15.895 0.418 16.375 KYCG_buildGeneDBs 15.316 0.453 15.854 testEnrichmentSEA 14.007 0.894 14.974 matchDesign 14.000 0.797 14.893 sesameQC_plotBetaByDesign 13.183 0.930 14.191 visualizeGene 13.213 0.475 13.810 sdf_read_table 10.953 0.411 11.476 compareMouseStrainReference 10.501 0.498 11.512 dyeBiasCorrMostBalanced 9.767 0.254 10.255 DML 9.138 0.859 10.112 compareReference 9.310 0.441 10.429 inferStrain 8.853 0.464 9.387 dbStats 8.583 0.511 9.154 estimateLeukocyte 8.626 0.411 9.070 getMask 8.544 0.480 9.077 DMR 8.785 0.218 9.044 createUCSCtrack 7.906 0.423 8.396 dyeBiasNL 7.721 0.491 8.251 bisConversionControl 7.857 0.238 8.299 inferTissue 7.339 0.731 8.098 probeSuccessRate 7.388 0.551 7.963 testEnrichment 6.908 0.757 7.733 KYCG_plotSetEnrichment 6.459 0.483 6.996 openSesame 6.105 0.559 6.710 deidentify 5.883 0.330 6.237 updateSigDF 5.049 0.316 5.405 print.DMLSummary 4.669 0.551 5.247 * 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