############################################################################## ############################################################################## ### ### 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_1.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 12.7.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.22.1’ * 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 189.158 8.133 237.737 imputeBetasByGenomicNeighbors 62.576 1.709 74.361 inferSex 38.817 1.270 44.888 sesameQC_calcStats 36.699 2.169 44.536 KYCG_plotMeta 36.411 1.215 45.802 sesameQC_plotHeatSNPs 32.388 1.781 37.495 imputeBetas 31.894 1.794 39.445 compareMouseStrainReference 32.650 0.998 39.369 KYCG_plotEnrichAll 31.979 1.430 38.270 compareReference 29.725 0.870 35.646 KYCG_annoProbes 25.347 1.353 31.231 ELBAR 23.389 2.710 29.637 diffRefSet 24.720 0.903 30.000 matchDesign 22.910 1.156 27.576 inferSpecies 21.028 1.090 25.154 sesameQC_plotBar 20.664 0.825 24.654 getRefSet 20.783 0.696 25.144 KYCG_plotMetaEnrichment 20.256 0.722 23.340 DML 17.791 2.054 25.169 testEnrichmentSEA 17.155 0.964 21.447 visualizeGene 17.395 0.683 21.168 KYCG_buildGeneDBs 17.396 0.653 21.941 DMR 17.002 0.524 20.858 sdf_read_table 16.545 0.766 19.756 sesameQC_plotBetaByDesign 15.903 1.371 19.062 deidentify 14.885 0.506 17.929 inferStrain 14.338 1.008 17.492 inferTissue 12.698 1.413 15.690 reIdentify 12.994 0.348 15.162 estimateLeukocyte 12.317 0.628 15.032 getMask 12.098 0.780 15.540 dbStats 10.704 0.899 13.716 KYCG_plotSetEnrichment 10.845 0.565 13.324 openSesame 9.959 0.745 12.200 createUCSCtrack 10.144 0.479 12.420 testEnrichment 9.424 1.006 11.632 probeSuccessRate 9.581 0.839 11.917 dyeBiasCorrMostBalanced 9.922 0.394 12.142 dyeBiasNL 8.565 0.543 10.787 bisConversionControl 7.809 0.304 9.210 prepSesame 7.493 0.469 9.019 visualizeProbes 6.872 0.202 8.165 scrubSoft 5.471 1.301 7.444 sesameQC_rankStats 5.960 0.537 7.344 updateSigDF 6.075 0.418 7.715 noMasked 6.121 0.329 7.605 sdf_write_table 5.833 0.352 6.964 KYCG_plotWaterfall 5.722 0.251 6.790 parseGEOsignalMU 5.334 0.617 6.873 print.DMLSummary 4.731 1.065 6.785 mapToMammal40 5.275 0.501 6.791 summaryExtractTest 4.681 0.983 6.451 meanIntensity 4.830 0.613 6.562 KYCG_getDBs 5.014 0.375 6.203 totalIntensities 4.982 0.317 6.234 detectionPnegEcdf 5.056 0.232 6.431 dyeBiasCorr 4.863 0.312 6.283 checkLevels 4.652 0.353 6.080 KYCG_plotPointRange 4.716 0.243 5.666 sesame-package 4.353 0.540 5.746 qualityMask 4.244 0.574 5.633 dyeBiasL 4.016 0.193 5.135 * 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