############################################################################## ############################################################################## ### ### 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: 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 ‘1.22.2’ * 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 174.643 7.950 216.705 imputeBetasByGenomicNeighbors 62.375 1.723 72.220 inferSex 37.950 1.282 44.473 sesameQC_calcStats 35.614 2.320 43.745 KYCG_plotMeta 34.077 1.186 40.852 compareMouseStrainReference 31.561 0.999 52.034 KYCG_plotEnrichAll 30.603 1.519 38.892 imputeBetas 29.233 1.785 36.011 sesameQC_plotHeatSNPs 28.537 1.665 36.009 compareReference 28.823 0.821 35.857 KYCG_annoProbes 24.460 1.364 30.209 diffRefSet 24.193 0.916 29.644 ELBAR 22.275 2.689 29.139 matchDesign 21.742 1.021 25.589 inferSpecies 21.444 1.106 25.513 getRefSet 19.568 0.680 22.944 sesameQC_plotBar 18.920 0.506 23.095 KYCG_plotMetaEnrichment 18.679 0.738 22.371 DML 17.134 1.768 21.913 testEnrichmentSEA 16.992 1.144 22.081 sesameQC_plotBetaByDesign 16.130 1.547 21.137 sdf_read_table 16.090 1.467 20.046 DMR 16.508 0.469 20.102 KYCG_buildGeneDBs 16.247 0.722 20.071 visualizeGene 15.776 0.616 19.863 inferStrain 14.707 0.986 19.851 deidentify 14.585 0.503 17.869 inferTissue 11.593 1.743 15.208 reIdentify 12.324 0.334 14.467 estimateLeukocyte 11.785 0.676 17.592 getMask 11.291 0.726 14.459 openSesame 10.322 1.194 13.309 dbStats 10.356 0.802 13.386 KYCG_plotSetEnrichment 9.849 0.529 11.963 createUCSCtrack 9.864 0.467 12.145 testEnrichment 8.917 1.075 11.800 dyeBiasCorrMostBalanced 9.423 0.392 11.686 probeSuccessRate 8.799 0.801 11.314 updateSigDF 8.657 0.635 11.628 dyeBiasNL 8.165 0.510 10.256 sesameQC_rankStats 6.923 0.799 9.136 bisConversionControl 7.156 0.296 8.502 prepSesame 6.802 0.527 9.010 noMasked 5.869 0.339 7.290 scrubSoft 5.138 0.957 6.944 sdf_write_table 5.572 0.355 6.858 totalIntensities 5.145 0.399 7.137 summaryExtractTest 4.272 1.153 6.536 KYCG_plotWaterfall 5.124 0.250 6.215 print.DMLSummary 4.355 1.011 6.458 mapToMammal40 4.861 0.477 6.116 detectionPnegEcdf 5.056 0.209 6.307 KYCG_getDBs 4.871 0.374 6.633 parseGEOsignalMU 4.970 0.221 6.042 meanIntensity 4.557 0.490 5.839 dyeBiasCorr 4.639 0.317 5.973 checkLevels 4.383 0.326 8.549 KYCG_plotPointRange 4.156 0.234 5.226 qualityMask 3.812 0.545 5.087 * 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