############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings sesame_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck' * using R version 4.3.3 (2024-02-29 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 12.3.0 GNU Fortran (GCC) 12.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'sesame/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'sesame' version '1.20.0' * 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 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 ... 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 114.72 4.74 126.84 sesameQC_calcStats 27.14 0.88 28.03 sesameQC_plotHeatSNPs 26.79 1.01 27.84 KYCG_plotEnrichAll 19.89 1.34 22.51 KYCG_plotMeta 20.27 0.63 21.50 matchDesign 18.61 0.69 19.33 inferSpecies 17.39 0.70 18.92 ELBAR 16.03 1.55 17.89 sdf_read_table 15.78 0.52 16.38 KYCG_annoProbes 14.53 0.95 15.89 testEnrichmentSEA 14.48 0.67 15.36 convertTo 14.42 0.55 16.53 sesameQC_plotBar 13.80 0.30 14.15 inferTissue 12.14 0.72 13.03 diffRefSet 12.09 0.66 13.81 compareReference 11.96 0.50 12.51 compareMouseStrainReference 11.71 0.68 12.60 getRefSet 12.00 0.39 12.46 sesameQC_plotBetaByDesign 11.61 0.69 12.30 KYCG_buildGeneDBs 11.50 0.54 12.69 DML 9.18 1.88 11.16 KYCG_plotMetaEnrichment 10.25 0.59 10.94 visualizeGene 9.52 0.45 10.03 inferStrain 9.35 0.55 9.94 DMR 8.86 0.37 9.42 dbStats 8.54 0.67 9.64 getSexInfo 8.72 0.42 9.34 sdf_write_table 8.50 0.21 8.77 createUCSCtrack 8.14 0.37 8.77 estimateLeukocyte 7.20 0.43 8.28 testEnrichment 6.84 0.59 7.52 openSesame 6.45 0.56 7.13 deidentify 6.53 0.36 7.06 dyeBiasNL 6.30 0.29 6.61 KYCG_plotSetEnrichment 5.61 0.55 6.27 dyeBiasCorrMostBalanced 5.79 0.24 6.09 probeSuccessRate 5.60 0.36 6.04 inferSex 5.31 0.39 5.77 bisConversionControl 5.05 0.25 5.82 getMask 4.85 0.39 5.46 prepSesame 4.68 0.32 5.02 * 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: OK