############################################################################## ############################################################################## ### ### 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: 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 13.6.5 * 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 166.472 6.396 268.419 imputeBetasByGenomicNeighbors 50.170 1.322 72.243 KYCG_plotMeta 32.890 1.044 48.812 inferSex 31.208 0.937 47.674 sesameQC_plotHeatSNPs 27.921 1.007 44.381 KYCG_plotEnrichAll 27.328 1.405 41.329 imputeBetas 26.227 1.388 39.423 ELBAR 23.503 2.380 34.361 sesameQC_calcStats 24.451 1.314 37.513 inferSpecies 21.666 0.865 34.615 KYCG_annoProbes 19.818 0.905 29.815 diffRefSet 18.855 0.691 27.976 sesameQC_plotBar 18.663 0.459 28.286 KYCG_plotMetaEnrichment 16.958 0.703 26.737 getRefSet 16.919 0.533 23.856 testEnrichmentSEA 15.657 0.961 26.231 KYCG_buildGeneDBs 15.882 0.530 23.662 sesameQC_plotBetaByDesign 13.997 0.994 22.671 matchDesign 13.943 0.717 22.418 compareMouseStrainReference 13.359 0.555 20.053 inferStrain 13.181 0.610 21.313 visualizeGene 12.607 0.521 20.144 compareReference 12.281 0.501 18.233 inferTissue 10.751 1.204 17.808 DMR 11.459 0.338 18.114 estimateLeukocyte 11.244 0.513 17.349 sdf_read_table 10.348 0.821 17.296 dbStats 10.177 0.605 16.039 DML 9.601 1.007 15.582 getMask 9.275 0.631 14.693 testEnrichment 8.159 0.968 14.449 createUCSCtrack 8.433 0.516 12.373 dyeBiasCorrMostBalanced 8.275 0.349 12.632 KYCG_plotSetEnrichment 7.814 0.443 12.246 openSesame 7.566 0.664 13.332 probeSuccessRate 7.154 0.780 12.531 bisConversionControl 6.563 0.281 10.128 dyeBiasNL 6.507 0.311 9.663 visualizeRegion 6.443 0.088 9.561 deidentify 5.853 0.479 9.419 prepSesame 5.327 0.368 9.633 print.DMLSummary 4.601 0.646 9.165 summaryExtractTest 4.647 0.590 8.782 mapToMammal40 4.388 0.675 8.316 reIdentify 4.869 0.193 7.936 totalIntensities 4.563 0.297 7.890 sesameQC_rankStats 4.323 0.269 7.356 noMasked 4.259 0.280 7.407 dyeBiasL 4.274 0.140 6.417 checkLevels 4.140 0.264 6.311 aggregateTestEnrichments 4.013 0.101 5.814 KYCG_plotWaterfall 3.865 0.235 6.067 parseGEOsignalMU 3.677 0.269 6.304 updateSigDF 3.611 0.307 6.286 KYCG_getDBs 3.609 0.297 5.795 KYCG_plotPointRange 3.638 0.217 5.706 meanIntensity 3.362 0.405 6.015 qualityMask 3.332 0.370 5.327 scrubSoft 3.184 0.515 5.104 visualizeSegments 3.163 0.520 6.182 dyeBiasCorr 3.282 0.272 5.130 predictAge 3.295 0.171 5.363 * 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