############################################################################## ############################################################################## ### ### 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/meat/sesame.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.3 (clang-1403.0.22.14.1) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.6.4 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.18.4’ * 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 173.361 6.526 236.118 sesameQC_calcStats 37.981 1.761 48.613 KYCG_plotMeta 33.412 1.046 44.335 sesameQC_plotHeatSNPs 32.513 1.578 43.312 KYCG_plotEnrichAll 30.465 1.315 42.394 compareMouseStrainReference 29.723 0.540 38.934 compareReference 26.657 0.814 35.554 inferSpecies 25.258 1.095 33.831 ELBAR 22.487 2.761 33.658 matchDesign 23.871 1.162 33.146 diffRefSet 22.882 0.716 30.375 KYCG_annoProbes 21.978 0.996 30.883 sesameQC_plotBar 19.909 0.484 26.432 KYCG_plotMetaEnrichment 18.611 0.644 25.561 testEnrichmentSEA 18.267 0.950 24.342 getRefSet 18.498 0.670 25.096 sesameQC_plotBetaByDesign 17.744 1.048 23.893 inferTissue 16.302 1.479 23.587 DML 15.681 1.656 23.544 KYCG_buildGeneDBs 16.132 0.588 22.851 sdf_read_table 15.404 0.611 20.553 visualizeGene 15.469 0.543 20.231 DMR 15.552 0.427 21.475 getSexInfo 14.561 0.606 19.538 deidentify 13.706 0.460 18.901 inferStrain 12.707 0.875 17.590 reIdentify 12.107 0.344 17.342 estimateLeukocyte 9.939 0.546 14.246 dbStats 9.333 0.706 13.379 KYCG_plotSetEnrichment 9.390 0.524 12.912 dyeBiasNL 9.201 0.554 12.324 dyeBiasCorrMostBalanced 9.290 0.320 12.605 openSesame 8.730 0.774 12.438 createUCSCtrack 9.035 0.335 12.903 probeSuccessRate 8.490 0.672 12.209 testEnrichment 8.068 0.558 12.218 inferSex 8.027 0.470 10.982 getMask 7.583 0.518 10.991 bisConversionControl 7.487 0.295 10.154 visualizeProbes 7.512 0.238 9.618 prepSesame 6.246 0.427 8.585 sdf_write_table 5.733 0.324 7.543 scrubSoft 5.365 0.644 7.568 sesameQC_rankStats 5.678 0.303 8.139 inferSexKaryotypes 5.361 0.260 7.238 formatVCF 5.237 0.374 7.368 KYCG_plotWaterfall 5.002 0.206 7.060 totalIntensities 4.770 0.386 6.514 KYCG_getDBs 4.774 0.340 6.883 mapToMammal40 4.700 0.384 7.100 print.DMLSummary 3.949 1.027 6.437 updateSigDF 4.625 0.302 6.400 detectionPnegEcdf 4.714 0.159 6.704 parseGEOsignalMU 4.651 0.197 6.078 checkLevels 4.407 0.428 6.325 dyeBiasCorr 4.326 0.264 6.146 meanIntensity 4.183 0.314 5.873 summaryExtractTest 3.728 0.692 6.136 qualityMask 3.741 0.469 6.334 scrub 3.844 0.297 5.488 sesameQC_getStats 3.933 0.188 5.083 sesame-package 3.643 0.458 5.063 KYCG_plotPointRange 3.821 0.212 5.218 inferEthnicity 3.675 0.245 5.244 noMasked 3.271 0.467 5.095 * 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/meat/sesame.Rcheck/00check.log’ for details.