############################################################################## ############################################################################## ### ### 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_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’ * using R version 4.3.2 Patched (2023-11-01 r85457) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) 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 ‘1.20.0’ * 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 R 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 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 126.297 5.667 134.786 sesameQC_calcStats 24.795 2.163 27.154 KYCG_plotMeta 24.229 1.060 25.632 KYCG_plotEnrichAll 20.514 1.062 22.164 sesameQC_plotHeatSNPs 19.894 1.551 21.816 ELBAR 16.903 3.266 20.441 inferSpecies 17.111 0.791 18.273 convertTo 15.089 0.399 15.666 KYCG_annoProbes 14.351 0.875 15.501 testEnrichmentSEA 13.677 1.171 15.343 matchDesign 13.833 0.824 14.802 sesameQC_plotBar 13.531 0.567 14.352 diffRefSet 13.246 0.572 14.054 compareMouseStrainReference 13.343 0.410 13.987 sesameQC_plotBetaByDesign 11.814 1.619 13.504 getRefSet 12.737 0.613 13.511 inferTissue 10.851 1.554 12.869 compareReference 11.668 0.647 12.588 KYCG_plotMetaEnrichment 11.266 0.608 12.144 KYCG_buildGeneDBs 11.281 0.485 11.989 visualizeGene 10.555 0.547 11.448 getSexInfo 9.877 0.633 10.904 DML 8.953 1.355 10.799 DMR 9.500 0.386 10.174 sdf_read_table 9.159 0.423 9.758 inferStrain 8.471 0.758 9.403 estimateLeukocyte 8.135 0.598 8.886 dbStats 7.246 0.747 8.144 createUCSCtrack 7.501 0.327 7.971 dyeBiasNL 6.862 0.609 7.605 dyeBiasCorrMostBalanced 6.995 0.302 7.490 testEnrichment 6.233 0.846 7.269 KYCG_plotSetEnrichment 6.391 0.623 7.185 openSesame 5.753 1.149 7.044 probeSuccessRate 6.416 0.469 7.188 deidentify 6.382 0.363 6.993 getMask 5.727 0.411 6.328 bisConversionControl 5.558 0.273 6.164 inferSex 5.060 0.482 5.673 reIdentify 5.148 0.375 5.620 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK