############################################################################## ############################################################################## ### ### 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_1.18.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sesame.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-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 12.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.18.4’ * 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 ... WARNING '::' or ':::' import not declared from: ‘BiocManager’ * 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 145.560 4.786 285.599 KYCG_plotMeta 25.007 0.763 47.042 sesameQC_plotHeatSNPs 24.276 0.800 45.057 sesameQC_calcStats 23.608 1.028 45.229 KYCG_plotEnrichAll 23.581 0.979 47.042 inferSpecies 18.344 0.725 34.708 matchDesign 17.607 0.590 33.236 testEnrichmentSEA 15.606 1.573 32.915 sesameQC_plotBar 15.835 1.018 30.609 ELBAR 15.408 1.062 27.642 KYCG_annoProbes 15.526 0.580 29.860 diffRefSet 15.245 0.453 27.745 compareMouseStrainReference 14.583 0.493 27.299 getRefSet 13.987 0.417 26.517 KYCG_plotMetaEnrichment 12.766 0.439 23.861 KYCG_buildGeneDBs 12.012 0.475 22.956 inferTissue 11.753 0.642 23.422 visualizeGene 11.829 0.561 23.867 compareReference 11.837 0.448 21.719 sesameQC_plotBetaByDesign 11.286 0.767 20.736 getSexInfo 11.311 0.467 24.610 sdf_read_table 10.565 0.682 21.074 DMR 9.950 0.277 18.690 DML 9.118 0.992 24.864 inferStrain 9.099 0.500 18.505 createUCSCtrack 8.389 0.361 16.303 probeSuccessRate 8.189 0.478 16.687 testEnrichment 7.863 0.556 16.537 dbStats 7.656 0.406 15.240 estimateLeukocyte 7.591 0.336 14.551 dyeBiasCorrMostBalanced 7.179 0.254 13.898 getMask 7.043 0.371 15.256 dyeBiasNL 7.057 0.188 13.190 openSesame 6.680 0.518 13.931 deidentify 6.770 0.349 13.758 KYCG_plotSetEnrichment 6.553 0.286 12.732 updateSigDF 5.943 0.500 12.493 mapToMammal40 5.656 0.417 11.757 reIdentify 5.753 0.172 10.898 visualizeProbes 5.550 0.263 11.019 bisConversionControl 5.593 0.205 11.034 inferSex 5.311 0.213 10.423 inferSexKaryotypes 5.197 0.131 8.888 print.DMLSummary 4.143 0.617 9.265 sesameQC_rankStats 4.389 0.236 8.959 formatVCF 4.155 0.296 8.847 KYCG_plotPointRange 4.288 0.158 7.472 KYCG_getDBs 4.166 0.255 8.798 sesame-package 3.791 0.539 8.038 prepSesame 4.006 0.267 8.305 totalIntensities 3.728 0.427 8.468 qualityMask 3.630 0.235 7.309 parseGEOsignalMU 3.580 0.219 7.535 scrubSoft 3.406 0.392 6.533 predictAge 3.436 0.199 7.007 sdf_write_table 3.328 0.298 6.945 checkLevels 3.383 0.186 6.761 meanIntensity 3.294 0.234 13.573 summaryExtractTest 3.174 0.310 7.270 dyeBiasCorr 3.253 0.196 6.688 KYCG_plotWaterfall 3.236 0.153 6.407 detectionPnegEcdf 3.140 0.134 6.358 inferEthnicity 2.959 0.158 5.594 listAvailableMasks 2.547 0.213 5.159 noMasked 2.443 0.245 5.293 sesameQC_plotIntensVsBetas 2.529 0.098 5.279 controls 2.415 0.174 5.499 * 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: 1 WARNING See ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/sesame.Rcheck/00check.log’ for details.