############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings sesame_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * 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 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 loading without being on the library search path ... 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 102.347 6.204 111.739 sesameQC_calcStats 18.783 1.436 20.387 KYCG_plotEnrichAll 17.908 1.689 20.724 KYCG_plotMeta 18.633 0.962 20.068 inferSpecies 17.301 1.928 19.711 sesameQC_plotHeatSNPs 16.790 1.088 18.076 ELBAR 14.909 1.008 16.076 matchDesign 14.627 0.831 15.650 KYCG_annoProbes 12.688 0.896 14.109 convertTo 12.708 0.736 13.765 sesameQC_plotBar 11.929 1.247 13.664 testEnrichmentSEA 11.297 1.424 13.135 diffRefSet 11.740 0.760 12.816 inferTissue 11.107 1.308 12.894 compareReference 11.206 1.148 12.670 getRefSet 11.394 0.783 12.518 compareMouseStrainReference 11.328 0.513 12.062 KYCG_buildGeneDBs 9.639 0.636 10.591 visualizeGene 9.469 0.780 10.784 sesameQC_plotBetaByDesign 9.394 0.580 9.974 DMR 9.298 0.560 10.218 KYCG_plotMetaEnrichment 9.393 0.432 10.296 sdf_read_table 8.743 0.400 9.462 getSexInfo 8.524 0.481 9.485 inferStrain 7.599 0.912 8.826 dbStats 7.036 1.024 8.380 createUCSCtrack 6.966 0.832 8.019 estimateLeukocyte 6.818 0.752 7.900 DML 7.157 0.337 7.850 probeSuccessRate 6.695 0.584 7.749 dyeBiasCorrMostBalanced 6.505 0.268 7.087 testEnrichment 6.105 0.556 7.135 dyeBiasNL 5.769 0.388 6.314 deidentify 5.714 0.381 6.413 openSesame 5.606 0.460 6.514 sesameQC_rankStats 5.236 0.567 6.125 getMask 4.989 0.412 5.916 KYCG_plotSetEnrichment 4.961 0.404 5.682 bisConversionControl 4.668 0.695 5.722 reIdentify 4.606 0.527 5.290 * 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 ... ‘KYCG.Rmd’ using ‘UTF-8’... OK ‘QC.Rmd’ using ‘UTF-8’... OK ‘inferences.Rmd’ using ‘UTF-8’... OK ‘modeling.Rmd’ using ‘UTF-8’... OK ‘nonhuman.Rmd’ using ‘UTF-8’... OK ‘sesame.Rmd’ using ‘UTF-8’... OK OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK