############################################################################## ############################################################################## ### ### 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_1.23.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * 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 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.6’ * 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 67.016 3.272 75.268 imputeBetasByGenomicNeighbors 46.111 1.274 48.797 inferSex 28.008 0.905 29.818 sesameQC_calcStats 25.502 1.983 28.114 KYCG_plotMeta 26.176 1.044 28.520 KYCG_plotEnrichAll 25.343 0.991 29.231 imputeBetas 23.927 1.442 29.980 sesameQC_plotHeatSNPs 21.918 1.478 23.866 sesameQC_plotBar 19.858 0.457 21.175 ELBAR 16.433 2.828 19.843 inferSpecies 18.427 0.719 20.493 KYCG_annoProbes 17.485 0.724 19.739 diffRefSet 17.511 0.631 18.987 getRefSet 16.731 0.428 20.886 KYCG_plotMetaEnrichment 15.647 0.559 17.773 KYCG_buildGeneDBs 14.925 0.488 16.741 testEnrichmentSEA 14.064 1.020 16.251 matchDesign 14.245 0.743 15.441 visualizeGene 13.913 0.448 15.531 sesameQC_plotBetaByDesign 12.260 1.497 13.813 compareMouseStrainReference 12.604 0.605 14.117 compareReference 11.409 0.379 12.815 inferStrain 11.251 0.495 12.612 sdf_read_table 11.027 0.669 12.533 DMR 9.921 0.235 10.948 dyeBiasCorrMostBalanced 9.781 0.271 10.858 estimateLeukocyte 9.481 0.418 11.417 DML 8.581 0.840 10.588 getMask 8.780 0.517 12.520 inferTissue 8.032 1.075 10.056 createUCSCtrack 8.340 0.398 9.529 dbStats 7.729 0.491 9.035 probeSuccessRate 7.480 0.634 9.651 testEnrichment 7.102 0.654 8.877 bisConversionControl 7.508 0.213 8.509 openSesame 6.878 0.608 8.332 KYCG_plotSetEnrichment 6.376 0.466 7.611 deidentify 6.049 0.376 7.241 dyeBiasNL 5.150 0.399 5.943 prepSesame 4.715 0.332 5.449 reIdentify 4.637 0.163 5.229 mapToMammal40 4.138 0.575 5.544 noMasked 4.461 0.216 5.486 summaryExtractTest 3.954 0.525 5.249 totalIntensities 4.166 0.255 5.187 updateSigDF 4.108 0.307 5.180 * 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