############################################################################## ############################################################################## ### ### 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: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.24.0’ * 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 65.861 4.048 70.853 imputeBetasByGenomicNeighbors 60.200 1.552 62.590 inferSex 39.326 1.376 41.104 sesameQC_calcStats 35.010 2.758 38.602 KYCG_plotMeta 32.345 1.089 34.066 sesameQC_plotHeatSNPs 30.754 1.702 33.066 compareMouseStrainReference 30.854 0.698 34.096 KYCG_plotEnrichAll 29.455 1.667 32.042 compareReference 28.322 1.076 30.296 imputeBetas 25.627 1.806 28.035 ELBAR 21.498 2.988 25.356 KYCG_annoProbes 23.373 1.107 25.035 diffRefSet 23.448 0.952 24.820 matchDesign 22.211 1.033 23.557 inferSpecies 20.692 0.865 21.879 getRefSet 19.615 0.712 20.663 sesameQC_plotBar 19.578 0.601 20.431 KYCG_plotMetaEnrichment 18.279 0.651 19.210 DML 17.065 1.647 19.575 sesameQC_plotBetaByDesign 16.260 0.989 17.489 testEnrichmentSEA 15.848 1.289 17.633 KYCG_buildGeneDBs 16.288 0.605 17.349 sdf_read_table 15.949 0.649 17.046 visualizeGene 15.681 0.753 16.555 DMR 15.259 0.381 16.339 deidentify 14.449 0.477 15.259 inferStrain 13.441 0.821 14.416 reIdentify 12.573 0.318 13.276 inferTissue 11.221 1.379 12.763 dbStats 10.728 0.846 11.777 dyeBiasNL 10.582 0.591 11.341 estimateLeukocyte 10.425 0.683 11.460 getMask 10.394 0.684 11.190 openSesame 9.397 1.104 10.850 createUCSCtrack 9.705 0.489 10.671 KYCG_plotSetEnrichment 9.498 0.600 10.262 dyeBiasCorrMostBalanced 9.309 0.419 9.888 testEnrichment 8.463 1.143 9.727 probeSuccessRate 8.626 0.860 9.561 bisConversionControl 7.162 0.298 22.188 noMasked 6.117 0.686 6.932 visualizeProbes 6.591 0.097 6.727 prepSesame 6.366 0.231 6.662 scrubSoft 5.227 1.241 6.575 KYCG_plotWaterfall 6.047 0.349 6.640 sdf_write_table 5.868 0.304 6.224 sesameQC_rankStats 5.482 0.587 6.143 print.DMLSummary 4.721 1.289 6.079 updateSigDF 5.424 0.425 5.906 parseGEOsignalMU 5.028 0.797 5.894 summaryExtractTest 4.180 1.160 5.863 detectionPnegEcdf 4.861 0.242 5.244 totalIntensities 4.666 0.419 5.232 dyeBiasCorr 4.681 0.336 5.063 KYCG_getDBs 4.629 0.371 5.271 * 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