############################################################################## ############################################################################## ### ### 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 39.452 0.856 40.311 imputeBetasByGenomicNeighbors 31.296 0.539 31.838 inferSex 21.833 0.094 21.928 KYCG_plotMeta 18.774 0.192 18.968 sesameQC_calcStats 17.537 0.256 17.794 KYCG_plotEnrichAll 16.961 0.620 17.584 imputeBetas 17.019 0.421 17.473 sesameQC_plotHeatSNPs 15.648 0.092 15.742 inferSpecies 13.988 0.649 14.638 diffRefSet 12.633 0.242 12.875 ELBAR 12.594 0.262 12.857 KYCG_annoProbes 11.157 0.193 11.351 sesameQC_plotBar 10.887 0.196 11.083 matchDesign 10.706 0.051 10.763 KYCG_plotMetaEnrichment 10.230 0.223 10.454 compareMouseStrainReference 10.281 0.125 10.416 getRefSet 10.240 0.138 10.378 compareReference 9.767 0.241 10.027 sesameQC_plotBetaByDesign 9.788 0.161 9.951 testEnrichmentSEA 9.102 0.226 9.327 KYCG_buildGeneDBs 8.915 0.235 9.150 visualizeGene 9.023 0.106 9.129 inferTissue 7.649 0.145 7.795 inferStrain 6.948 0.314 7.265 estimateLeukocyte 7.156 0.098 7.256 sdf_read_table 7.087 0.152 7.239 DML 6.857 0.366 7.229 DMR 6.804 0.218 7.022 getMask 5.959 0.135 6.098 dyeBiasNL 5.750 0.096 5.849 dbStats 5.600 0.132 5.734 testEnrichment 5.533 0.100 5.634 dyeBiasCorrMostBalanced 5.476 0.112 5.589 createUCSCtrack 5.136 0.063 5.200 deidentify 4.929 0.093 5.023 * 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