############################################################################## ############################################################################## ### ### 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_1.22.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.22.2’ * 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 166.284 6.213 184.789 imputeBetasByGenomicNeighbors 45.271 1.723 53.389 inferSex 30.618 1.114 33.961 sesameQC_calcStats 26.181 2.589 30.112 KYCG_plotMeta 27.313 1.173 31.967 KYCG_plotEnrichAll 26.993 1.058 31.912 imputeBetas 24.099 2.093 28.650 sesameQC_plotHeatSNPs 22.659 1.342 25.616 ELBAR 16.908 3.579 21.368 sesameQC_plotBar 19.405 0.489 21.818 inferSpecies 18.382 0.824 21.481 diffRefSet 17.821 0.845 22.058 KYCG_annoProbes 17.864 0.754 20.769 getRefSet 17.293 0.609 19.997 KYCG_plotMetaEnrichment 16.409 0.715 21.293 KYCG_buildGeneDBs 15.466 0.580 17.815 visualizeGene 14.240 0.575 16.237 sesameQC_plotBetaByDesign 12.654 2.148 15.849 matchDesign 13.971 0.799 15.563 testEnrichmentSEA 13.909 0.855 16.118 compareMouseStrainReference 13.388 0.612 16.519 compareReference 12.195 0.490 14.850 sdf_read_table 11.367 0.721 13.058 inferStrain 10.880 0.726 12.827 DMR 10.580 0.290 11.922 estimateLeukocyte 9.936 0.494 12.708 dyeBiasCorrMostBalanced 10.077 0.351 12.460 DML 9.123 0.932 11.218 getMask 9.423 0.553 12.897 dbStats 8.803 0.711 11.436 createUCSCtrack 8.764 0.472 11.258 openSesame 7.440 0.848 9.331 testEnrichment 7.542 0.730 9.895 bisConversionControl 7.753 0.246 9.676 probeSuccessRate 7.366 0.628 10.320 inferTissue 6.398 1.037 8.897 KYCG_plotSetEnrichment 6.407 0.587 8.786 deidentify 5.862 0.370 7.578 dyeBiasNL 5.210 0.641 6.953 mapToMammal40 4.772 0.451 6.162 noMasked 4.653 0.340 5.924 prepSesame 4.586 0.322 5.657 reIdentify 4.724 0.147 5.854 totalIntensities 4.435 0.269 5.553 parseGEOsignalMU 4.327 0.238 5.052 summaryExtractTest 3.987 0.538 5.828 print.DMLSummary 3.795 0.505 5.237 sesameQC_rankStats 3.809 0.362 5.104 * 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