############################################################################## ############################################################################## ### ### 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_1.21.12.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R Under development (unstable) (2024-01-16 r85808) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.21.12’ * 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 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 176.358 7.695 216.738 inferSex 54.830 2.057 66.562 sesameQC_calcStats 34.887 1.631 42.412 KYCG_plotMeta 32.151 1.307 39.819 KYCG_plotEnrichAll 29.770 1.572 38.615 compareMouseStrainReference 30.048 0.899 37.495 sesameQC_plotHeatSNPs 29.049 1.293 35.065 compareReference 27.188 1.150 32.918 matchDesign 23.919 1.124 29.379 ELBAR 21.927 2.938 30.698 KYCG_annoProbes 23.091 1.127 29.319 diffRefSet 23.110 0.947 29.573 inferSpecies 21.250 1.225 26.542 sesameQC_plotBar 19.736 0.513 23.745 KYCG_plotMetaEnrichment 18.828 0.926 23.666 DML 16.966 2.662 31.976 getRefSet 18.377 0.693 22.383 sesameQC_plotBetaByDesign 16.648 1.959 22.239 KYCG_buildGeneDBs 16.313 0.652 20.006 sdf_read_table 15.716 0.991 19.864 testEnrichmentSEA 15.562 0.933 20.388 visualizeGene 15.357 0.655 19.399 DMR 14.964 0.449 19.397 deidentify 14.047 0.496 18.034 inferStrain 12.906 0.935 15.917 inferTissue 11.157 1.495 14.709 estimateLeukocyte 11.477 0.650 14.209 reIdentify 11.762 0.348 14.105 dbStats 9.955 0.870 13.375 KYCG_plotSetEnrichment 9.601 0.627 12.079 openSesame 9.249 0.920 12.050 createUCSCtrack 9.485 0.453 11.955 dyeBiasNL 9.305 0.611 11.967 dyeBiasCorrMostBalanced 9.224 0.418 11.575 testEnrichment 8.614 0.846 11.266 probeSuccessRate 8.689 0.540 11.164 getMask 7.997 0.549 10.160 bisConversionControl 7.180 0.338 12.890 prepSesame 6.159 0.218 7.540 sesameQC_rankStats 5.770 0.356 7.153 scrubSoft 5.168 0.818 6.972 print.DMLSummary 4.734 1.048 6.929 parseGEOsignalMU 5.107 0.571 6.746 summaryExtractTest 4.615 1.016 6.696 sdf_write_table 5.048 0.391 6.560 qualityMask 4.792 0.642 6.592 updateSigDF 4.968 0.370 6.485 KYCG_plotWaterfall 5.079 0.257 6.866 totalIntensities 4.958 0.340 6.318 mapToMammal40 4.749 0.426 6.268 KYCG_getDBs 4.731 0.409 6.623 detectionPnegEcdf 4.929 0.209 6.187 dyeBiasCorr 4.532 0.341 6.102 meanIntensity 4.488 0.324 6.162 checkLevels 4.399 0.373 7.545 * 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