############################################################################## ############################################################################## ### ### 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * 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 ‘1.24.0’ * 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 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 37.602 0.734 38.340 imputeBetasByGenomicNeighbors 30.445 0.575 31.042 inferSex 20.717 0.311 21.029 KYCG_plotMeta 19.068 0.214 19.284 sesameQC_calcStats 17.399 0.230 17.630 KYCG_plotEnrichAll 16.885 0.595 17.484 imputeBetas 16.610 0.374 17.013 sesameQC_plotHeatSNPs 15.893 0.093 15.990 inferSpecies 12.974 0.636 13.611 ELBAR 13.104 0.300 13.407 diffRefSet 12.346 0.163 12.510 KYCG_annoProbes 11.659 0.214 11.874 sesameQC_plotBar 10.760 0.130 10.890 KYCG_plotMetaEnrichment 10.401 0.239 10.642 matchDesign 10.549 0.083 10.637 compareMouseStrainReference 10.195 0.149 10.346 getRefSet 10.219 0.068 10.288 compareReference 9.614 0.201 9.814 sesameQC_plotBetaByDesign 9.498 0.148 9.648 testEnrichmentSEA 9.155 0.179 9.334 KYCG_buildGeneDBs 9.139 0.175 9.318 visualizeGene 8.837 0.117 8.954 inferTissue 7.596 0.243 7.841 sdf_read_table 7.427 0.103 7.530 estimateLeukocyte 7.352 0.109 7.462 DML 6.986 0.320 7.307 DMR 7.026 0.192 7.220 inferStrain 6.857 0.331 7.192 dbStats 5.544 0.212 5.759 dyeBiasNL 5.670 0.051 5.723 getMask 5.575 0.098 5.675 dyeBiasCorrMostBalanced 5.464 0.084 5.549 deidentify 4.968 0.112 5.082 KYCG_plotSetEnrichment 4.939 0.101 5.040 openSesame 4.771 0.265 5.042 createUCSCtrack 4.971 0.064 5.036 testEnrichment 4.945 0.090 5.036 * 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