############################################################################## ############################################################################## ### ### 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-mac-arm64/meat/sesame.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * 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 13.6.1 * 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 175.219 5.528 195.484 KYCG_plotEnrichAll 28.014 1.141 33.895 KYCG_plotMeta 25.915 1.285 30.406 sesameQC_calcStats 25.174 1.374 28.439 sesameQC_plotHeatSNPs 23.300 1.990 26.979 inferSpecies 22.619 0.961 26.196 convertTo 22.482 0.590 24.576 sesameQC_plotBar 21.381 0.686 24.238 matchDesign 19.801 1.083 22.329 ELBAR 15.999 3.359 20.070 testEnrichmentSEA 17.133 0.927 19.658 KYCG_annoProbes 17.022 0.608 19.269 diffRefSet 16.795 0.691 19.402 getRefSet 16.168 0.606 18.746 visualizeGene 15.280 0.489 17.284 KYCG_plotMetaEnrichment 14.284 0.628 16.928 KYCG_buildGeneDBs 14.019 0.429 15.394 getSexInfo 13.664 0.784 16.235 inferTissue 12.646 0.852 15.362 compareMouseStrainReference 12.314 0.476 14.292 compareReference 12.210 0.467 13.556 sesameQC_plotBetaByDesign 11.295 1.041 12.942 sdf_read_table 11.225 0.468 13.444 dyeBiasCorrMostBalanced 11.032 0.297 12.841 estimateLeukocyte 10.583 0.493 12.543 DMR 10.109 0.267 11.676 inferStrain 9.274 0.812 11.378 DML 8.386 0.846 10.253 createUCSCtrack 8.868 0.291 10.501 dbStats 8.280 0.593 9.975 probeSuccessRate 8.117 0.565 10.598 testEnrichment 7.941 0.704 10.112 bisConversionControl 8.027 0.283 9.803 getMask 7.597 0.437 10.191 KYCG_plotSetEnrichment 6.572 0.573 8.283 dyeBiasNL 6.382 0.714 8.172 deidentify 6.319 0.493 7.862 visualizeProbes 6.433 0.152 7.093 openSesame 6.131 0.450 7.923 inferSex 5.741 0.466 7.306 prepSesame 5.644 0.539 6.873 mapToMammal40 5.573 0.422 7.057 reIdentify 5.329 0.246 6.300 scrubSoft 3.950 1.138 5.378 qualityMask 4.625 0.414 6.073 parseGEOsignalMU 4.565 0.321 5.539 KYCG_plotPointRange 4.657 0.201 5.518 inferSexKaryotypes 4.575 0.271 5.486 summaryExtractTest 4.193 0.439 5.659 sesameQC_rankStats 4.038 0.516 5.545 totalIntensities 4.041 0.244 5.108 updateSigDF 3.878 0.245 5.196 KYCG_getDBs 3.853 0.234 5.140 * 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