############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings sesame_1.25.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’ * using R Under development (unstable) (2025-01-20 r87609) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.25.3’ * 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 loading without being on the library search path ... 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 imputeBetasByGenomicNeighbors 33.548 0.834 34.385 inferSex 20.797 0.376 21.176 imputeBetas 17.295 0.529 17.832 sesameQC_calcStats 17.333 0.206 17.541 sesameQC_plotHeatSNPs 16.611 0.235 16.849 inferSpecies 15.686 0.908 16.597 diffRefSet 13.886 0.321 14.211 ELBAR 13.664 0.201 13.867 getRefSet 11.134 0.264 11.399 sesameQC_plotBar 11.081 0.275 11.356 compareMouseStrainReference 10.886 0.237 11.124 matchDesign 10.943 0.178 11.127 compareReference 10.710 0.384 11.096 sesameQC_plotBetaByDesign 10.004 0.274 10.281 visualizeGene 8.596 0.394 8.991 DMR 8.354 0.339 8.695 inferStrain 7.261 0.512 7.776 sdf_read_table 7.350 0.220 7.569 estimateLeukocyte 7.289 0.225 7.517 DML 6.549 0.410 6.969 inferTissue 6.404 0.239 6.645 dyeBiasCorrMostBalanced 6.224 0.212 6.438 getMask 5.885 0.330 6.220 deidentify 5.799 0.171 5.974 createUCSCtrack 5.408 0.208 5.623 dyeBiasNL 5.323 0.162 5.486 probeSuccessRate 5.168 0.242 5.410 openSesame 5.002 0.247 5.256 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK