############################################################################## ############################################################################## ### ### 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 36.807 0.774 37.583 imputeBetasByGenomicNeighbors 31.501 0.477 32.001 inferSex 21.145 0.319 21.465 KYCG_plotMeta 19.046 0.191 19.248 sesameQC_calcStats 17.708 0.229 17.940 imputeBetas 16.739 0.393 17.137 KYCG_plotEnrichAll 16.398 0.582 16.986 sesameQC_plotHeatSNPs 14.750 0.040 14.792 inferSpecies 13.103 0.628 13.731 ELBAR 12.886 0.298 13.190 diffRefSet 12.308 0.187 12.495 KYCG_annoProbes 11.402 0.196 11.604 sesameQC_plotBar 10.708 0.127 10.834 KYCG_plotMetaEnrichment 10.577 0.199 10.776 matchDesign 10.563 0.191 10.757 getRefSet 10.336 0.068 10.405 compareMouseStrainReference 10.245 0.127 10.372 compareReference 9.602 0.240 9.842 KYCG_buildGeneDBs 9.165 0.311 9.491 sesameQC_plotBetaByDesign 9.391 0.051 9.445 visualizeGene 8.936 0.139 9.076 testEnrichmentSEA 8.864 0.180 9.045 inferTissue 7.357 0.144 7.502 sdf_read_table 7.219 0.101 7.320 estimateLeukocyte 7.212 0.098 7.310 DMR 7.047 0.217 7.263 DML 6.894 0.330 7.226 inferStrain 6.810 0.344 7.156 getMask 6.060 0.084 6.145 dbStats 5.581 0.213 5.796 dyeBiasNL 5.708 0.029 5.739 dyeBiasCorrMostBalanced 5.410 0.084 5.503 createUCSCtrack 5.002 0.094 5.096 deidentify 4.976 0.072 5.050 openSesame 4.792 0.218 5.019 * 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