############################################################################## ############################################################################## ### ### 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 39.959 0.869 41.958 imputeBetasByGenomicNeighbors 33.006 0.680 34.028 KYCG_plotMeta 24.748 0.216 25.136 inferSex 21.766 0.252 22.132 KYCG_plotEnrichAll 21.039 0.472 21.917 sesameQC_calcStats 18.253 0.180 18.488 ELBAR 17.667 0.348 18.173 imputeBetas 17.228 0.484 17.984 sesameQC_plotHeatSNPs 16.508 0.172 16.878 inferSpecies 15.462 0.596 16.430 KYCG_annoProbes 14.867 0.480 15.531 diffRefSet 13.790 0.124 14.138 KYCG_plotMetaEnrichment 12.504 0.276 13.050 compareMouseStrainReference 11.596 0.132 11.942 compareReference 11.335 0.288 11.845 sesameQC_plotBar 11.441 0.120 12.174 KYCG_buildGeneDBs 10.875 0.300 11.391 getRefSet 10.796 0.144 11.296 matchDesign 10.549 0.200 10.907 sesameQC_plotBetaByDesign 10.161 0.140 10.301 testEnrichmentSEA 9.936 0.180 10.389 DMR 9.337 0.235 9.929 visualizeGene 9.344 0.152 9.769 sdf_read_table 8.308 0.140 8.564 estimateLeukocyte 7.810 0.164 8.089 inferStrain 7.362 0.380 7.978 DML 7.329 0.320 7.966 getMask 7.114 0.148 7.699 dbStats 6.584 0.172 6.914 inferTissue 6.354 0.176 6.847 dyeBiasCorrMostBalanced 6.364 0.108 6.591 createUCSCtrack 6.238 0.068 6.521 dyeBiasNL 6.150 0.044 6.352 KYCG_plotSetEnrichment 5.830 0.139 6.183 testEnrichment 5.473 0.152 6.005 probeSuccessRate 5.516 0.104 5.891 deidentify 5.292 0.092 5.611 bisConversionControl 4.970 0.076 5.163 openSesame 4.910 0.128 5.255 * 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