############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sesame_1.23.8.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * 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 ‘1.23.8’ * 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 testEnrichmentGene 39.067 0.784 39.854 imputeBetasByGenomicNeighbors 30.698 1.848 32.565 KYCG_plotMeta 22.412 0.192 22.605 inferSex 20.264 0.628 20.891 KYCG_plotEnrichAll 18.566 0.508 19.076 sesameQC_calcStats 18.262 0.136 18.398 imputeBetas 17.156 0.576 17.736 sesameQC_plotHeatSNPs 16.811 0.196 17.007 ELBAR 15.279 0.236 15.515 inferSpecies 14.453 0.952 15.405 KYCG_annoProbes 13.389 0.436 13.846 diffRefSet 12.498 0.424 12.923 KYCG_plotMetaEnrichment 12.514 0.272 12.786 sesameQC_plotBar 12.352 0.320 12.673 compareMouseStrainReference 11.148 0.480 11.630 getRefSet 10.610 0.244 10.855 KYCG_buildGeneDBs 10.370 0.364 10.735 matchDesign 10.319 0.328 10.648 testEnrichmentSEA 10.321 0.088 10.410 compareReference 9.916 0.384 10.300 visualizeGene 9.510 0.200 9.710 sesameQC_plotBetaByDesign 9.232 0.108 9.340 sdf_read_table 8.213 0.116 8.329 DMR 7.931 0.204 8.136 inferStrain 6.854 0.364 7.217 DML 6.723 0.208 6.931 KYCG_plotSetEnrichment 6.142 0.468 6.610 estimateLeukocyte 6.398 0.172 6.570 dbStats 5.980 0.352 6.333 inferTissue 6.147 0.072 6.219 getMask 6.034 0.184 6.219 dyeBiasCorrMostBalanced 5.854 0.088 5.943 createUCSCtrack 5.567 0.168 5.735 dyeBiasNL 5.331 0.088 5.419 testEnrichment 5.192 0.200 5.393 probeSuccessRate 5.105 0.083 5.188 openSesame 4.960 0.208 5.171 deidentify 5.080 0.068 5.149 bisConversionControl 4.848 0.224 5.071 * 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