############################################################################## ############################################################################## ### ### 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 66.954 3.254 70.711 imputeBetasByGenomicNeighbors 42.621 1.163 44.168 inferSex 29.748 1.016 30.900 KYCG_plotMeta 26.415 1.061 27.699 sesameQC_calcStats 25.064 1.936 27.289 KYCG_plotEnrichAll 25.265 1.039 26.628 sesameQC_plotHeatSNPs 24.144 1.216 25.503 imputeBetas 21.932 1.475 23.530 sesameQC_plotBar 20.417 0.421 20.936 ELBAR 16.089 2.648 18.867 inferSpecies 17.438 0.769 18.302 diffRefSet 17.080 0.675 18.328 KYCG_annoProbes 16.994 0.643 17.781 KYCG_plotMetaEnrichment 15.970 0.545 16.818 getRefSet 15.971 0.496 16.545 KYCG_buildGeneDBs 15.315 0.454 15.853 matchDesign 14.639 0.747 15.475 testEnrichmentSEA 13.909 0.922 14.912 visualizeGene 13.580 0.439 14.078 compareReference 12.220 0.579 12.900 compareMouseStrainReference 12.229 0.486 12.807 sesameQC_plotBetaByDesign 10.968 0.739 11.752 DML 9.413 0.810 10.320 dyeBiasCorrMostBalanced 9.822 0.253 10.123 sdf_read_table 9.584 0.369 10.098 inferStrain 9.399 0.464 9.939 getMask 8.652 0.468 9.176 dbStats 8.549 0.500 9.112 DMR 8.808 0.222 9.069 estimateLeukocyte 8.550 0.392 9.010 inferTissue 8.128 0.793 8.972 createUCSCtrack 8.050 0.333 8.434 probeSuccessRate 7.520 0.662 8.230 dyeBiasNL 7.575 0.433 8.036 bisConversionControl 7.756 0.211 8.038 testEnrichment 6.716 0.635 7.441 KYCG_plotSetEnrichment 6.540 0.483 7.466 openSesame 6.028 0.523 6.655 deidentify 5.805 0.319 6.173 reIdentify 4.931 0.365 5.332 noMasked 4.684 0.363 5.069 prepSesame 4.725 0.306 5.052 * 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