############################################################################## ############################################################################## ### ### 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 4.3.3 (2024-02-29) * using platform: x86_64-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 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 175.243 7.356 196.168 sesameQC_calcStats 35.500 1.511 38.794 KYCG_plotMeta 33.043 1.225 36.879 KYCG_plotEnrichAll 29.863 1.509 33.709 sesameQC_plotHeatSNPs 28.876 1.964 32.417 compareMouseStrainReference 29.546 0.581 32.098 compareReference 26.005 0.778 28.387 ELBAR 21.755 3.220 25.825 matchDesign 23.773 0.953 25.910 inferSpecies 23.782 0.919 26.373 KYCG_annoProbes 22.294 0.975 25.114 diffRefSet 21.319 0.683 23.155 convertTo 20.780 0.775 22.628 sesameQC_plotBar 19.703 0.476 21.677 testEnrichmentSEA 18.667 1.071 21.108 sesameQC_plotBetaByDesign 17.587 1.490 20.213 getRefSet 18.382 0.621 23.090 DML 16.521 1.719 19.227 KYCG_plotMetaEnrichment 17.250 0.799 20.092 inferTissue 16.141 1.468 18.750 KYCG_buildGeneDBs 15.867 0.598 17.649 visualizeGene 15.817 0.583 18.107 sdf_read_table 14.756 0.845 21.661 DMR 14.262 0.429 15.082 getSexInfo 13.790 0.599 15.183 inferStrain 13.229 0.881 14.722 deidentify 13.479 0.481 14.680 dbStats 11.699 0.940 13.543 reIdentify 12.002 0.406 13.158 createUCSCtrack 11.338 0.411 12.562 dyeBiasNL 10.291 0.664 11.593 estimateLeukocyte 10.075 0.600 11.411 KYCG_plotSetEnrichment 9.479 0.597 10.840 probeSuccessRate 9.103 0.611 10.721 openSesame 9.103 0.571 10.391 dyeBiasCorrMostBalanced 9.222 0.342 10.433 testEnrichment 8.412 0.905 9.695 getMask 8.133 0.533 9.471 inferSex 7.775 0.477 8.690 bisConversionControl 7.496 0.345 8.324 visualizeProbes 7.388 0.211 8.310 KYCG_plotWaterfall 6.592 0.262 7.220 scrubSoft 5.544 0.839 6.609 print.DMLSummary 5.242 1.137 7.061 prepSesame 6.154 0.171 6.769 sesameQC_rankStats 5.327 0.538 6.232 KYCG_plotPointRange 5.291 0.259 6.580 sdf_write_table 5.164 0.383 8.659 parseGEOsignalMU 5.082 0.461 6.008 inferSexKaryotypes 5.016 0.289 5.611 totalIntensities 4.901 0.396 5.943 updateSigDF 4.914 0.355 5.984 detectionPnegEcdf 4.969 0.179 5.444 mapToMammal40 4.752 0.385 5.470 checkLevels 4.449 0.535 5.415 qualityMask 4.608 0.339 5.447 KYCG_getDBs 4.544 0.374 5.213 dyeBiasCorr 4.496 0.330 5.383 summaryExtractTest 4.065 0.743 5.301 meanIntensity 4.372 0.284 5.529 sesame-package 4.060 0.537 5.114 * 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