############################################################################## ############################################################################## ### ### 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 4.4.2 (2024-10-31) * 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 ‘1.24.0’ * 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 66.534 4.683 74.976 imputeBetasByGenomicNeighbors 58.243 1.686 63.732 inferSex 36.863 1.280 40.551 sesameQC_calcStats 35.034 2.233 39.811 KYCG_plotMeta 32.319 1.181 36.060 compareMouseStrainReference 31.005 0.641 36.559 sesameQC_plotHeatSNPs 29.051 1.629 32.844 KYCG_plotEnrichAll 28.948 1.643 32.960 compareReference 27.791 0.966 31.068 imputeBetas 26.592 1.788 30.489 ELBAR 22.652 2.812 27.744 KYCG_annoProbes 23.339 1.117 26.646 diffRefSet 23.381 0.891 26.071 matchDesign 21.183 1.218 23.654 inferSpecies 19.764 1.074 22.181 sesameQC_plotBar 19.463 0.543 21.346 KYCG_plotMetaEnrichment 18.525 0.745 20.843 getRefSet 18.394 0.612 20.264 DML 17.094 1.699 20.727 sesameQC_plotBetaByDesign 17.083 1.543 19.600 visualizeGene 17.111 1.043 20.624 testEnrichmentSEA 16.028 1.408 18.778 KYCG_buildGeneDBs 16.041 0.634 17.695 sdf_read_table 15.375 0.731 17.198 DMR 15.060 0.385 16.338 deidentify 14.003 0.457 15.432 inferStrain 12.527 0.760 13.995 inferTissue 10.563 1.502 12.741 reIdentify 11.700 0.339 12.680 dbStats 10.639 0.796 12.473 estimateLeukocyte 10.455 0.633 11.803 getMask 10.241 0.685 11.414 dyeBiasNL 10.362 0.563 11.477 openSesame 9.596 1.326 11.599 KYCG_plotSetEnrichment 9.750 0.633 11.092 createUCSCtrack 9.467 0.518 10.710 testEnrichment 8.395 1.256 14.698 dyeBiasCorrMostBalanced 9.172 0.368 10.178 probeSuccessRate 8.692 0.693 10.023 bisConversionControl 7.313 0.288 7.995 noMasked 6.166 0.766 7.335 parseGEOsignalMU 5.363 1.317 7.210 scrubSoft 5.232 1.225 6.935 prepSesame 6.035 0.335 6.884 updateSigDF 5.486 0.673 7.160 print.DMLSummary 4.665 1.281 6.301 sesameQC_rankStats 5.489 0.354 6.346 sdf_write_table 5.316 0.374 6.165 summaryExtractTest 4.157 1.169 5.808 checkLevels 4.647 0.493 5.446 totalIntensities 4.727 0.396 5.632 detectionPnegEcdf 4.904 0.212 5.447 KYCG_plotWaterfall 4.830 0.230 5.355 KYCG_getDBs 4.596 0.374 5.332 dyeBiasCorr 4.562 0.339 5.256 mapToMammal40 4.237 0.538 5.056 * 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