############################################################################## ############################################################################## ### ### 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 4.4.3 (2025-02-28) * using platform: aarch64-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 Ventura 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.24.0’ * 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 66.361 3.465 70.665 imputeBetasByGenomicNeighbors 43.056 1.530 45.484 inferSex 28.274 1.117 29.667 sesameQC_calcStats 25.106 1.978 27.378 KYCG_plotMeta 25.520 0.946 26.808 KYCG_plotEnrichAll 24.970 1.066 26.250 sesameQC_plotHeatSNPs 22.943 1.241 24.442 imputeBetas 21.496 1.658 23.779 sesameQC_plotBar 20.592 0.422 21.272 ELBAR 17.049 3.228 20.694 inferSpecies 17.760 0.796 18.740 diffRefSet 17.732 0.810 19.269 KYCG_annoProbes 17.068 0.699 17.909 getRefSet 16.298 0.633 17.542 testEnrichmentSEA 15.950 0.972 17.087 KYCG_plotMetaEnrichment 15.853 0.515 16.568 KYCG_buildGeneDBs 15.254 0.442 15.850 matchDesign 14.804 0.794 15.701 visualizeGene 14.194 0.468 14.784 compareMouseStrainReference 13.753 0.644 15.514 sesameQC_plotBetaByDesign 11.859 1.182 13.253 sdf_read_table 11.193 0.421 11.719 compareReference 10.830 0.523 12.105 DML 9.443 0.841 10.392 dyeBiasCorrMostBalanced 9.703 0.333 10.679 inferStrain 9.352 0.484 9.877 getMask 8.952 0.589 10.062 DMR 8.884 0.213 9.196 inferTissue 8.265 0.718 9.094 estimateLeukocyte 8.409 0.486 9.429 createUCSCtrack 8.228 0.466 9.145 dbStats 7.738 0.556 8.661 probeSuccessRate 7.383 0.683 8.110 bisConversionControl 7.753 0.226 8.112 testEnrichment 7.149 0.815 8.018 dyeBiasNL 7.359 0.451 8.366 openSesame 6.179 0.527 6.749 KYCG_plotSetEnrichment 6.158 0.497 6.948 deidentify 6.100 0.435 6.831 noMasked 4.678 0.412 5.147 scrubSoft 4.222 0.791 5.043 print.DMLSummary 4.387 0.596 5.007 * 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