############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings sesame_1.25.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/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 22.880 0.524 27.203 inferSex 14.667 0.204 16.640 sesameQC_calcStats 12.575 0.017 15.041 sesameQC_plotHeatSNPs 12.470 0.034 15.888 imputeBetas 11.968 0.300 14.000 ELBAR 10.859 0.167 14.957 inferSpecies 10.278 0.693 11.480 sesameQC_plotBar 9.410 0.100 10.365 diffRefSet 9.374 0.135 10.827 compareMouseStrainReference 8.106 0.080 8.504 compareReference 7.857 0.126 8.487 getRefSet 7.723 0.045 7.995 sesameQC_plotBetaByDesign 7.558 0.001 9.100 matchDesign 7.120 0.051 8.651 DMR 5.716 0.119 6.700 visualizeGene 5.311 0.087 5.891 estimateLeukocyte 5.032 0.116 5.815 DML 4.744 0.377 6.058 sdf_read_table 4.950 0.082 5.566 inferStrain 4.457 0.471 6.728 dyeBiasNL 4.780 0.083 5.260 inferTissue 4.302 0.094 6.079 * 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