############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings sesame_1.17.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.17.9’ * 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 R 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 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 123.124 8.543 135.150 KYCG_plotMeta 24.576 1.465 26.592 KYCG_plotEnrichAll 20.747 2.202 24.158 sesameQC_calcStats 21.181 1.264 22.610 sesameQC_plotHeatSNPs 19.308 1.236 20.709 inferSpecies 16.492 1.520 18.348 ELBAR 16.386 1.160 17.714 matchDesign 16.252 0.845 17.260 KYCG_annoProbes 14.205 1.474 16.183 diffRefSet 14.096 1.272 15.704 compareMouseStrainReference 13.853 0.989 15.176 compareReference 12.708 1.243 14.287 visualizeGene 11.485 1.388 13.374 sesameQC_plotBar 11.912 0.708 13.045 testEnrichmentSEA 10.776 1.536 12.820 KYCG_buildGeneDBs 11.008 1.197 12.538 getRefSet 10.857 0.835 12.025 KYCG_plotMetaEnrichment 10.933 0.707 12.140 sesameQC_plotBetaByDesign 10.874 0.676 11.550 inferTissue 10.247 1.200 11.968 dbStats 9.185 1.236 10.762 DMR 9.020 0.832 10.186 getSexInfo 9.167 0.605 10.268 sdf_read_table 8.939 0.564 9.930 createUCSCtrack 8.270 0.708 9.316 DML 7.777 0.708 8.822 dyeBiasNL 7.766 0.679 8.613 testEnrichment 7.366 0.871 8.741 inferStrain 7.143 0.896 8.369 visualizeProbes 7.232 0.644 8.082 estimateLeukocyte 6.914 0.655 7.805 deidentify 6.400 0.896 7.781 dyeBiasCorrMostBalanced 6.346 0.444 7.128 KYCG_plotSetEnrichment 6.077 0.580 7.014 reIdentify 5.786 0.840 6.794 bisConversionControl 5.713 0.500 6.755 inferSex 5.474 0.652 6.604 checkLevels 4.562 0.701 5.432 inferSexKaryotypes 4.602 0.452 5.218 sesameQC_rankStats 4.235 0.451 5.025 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘KYCG.Rmd’ using ‘UTF-8’... OK ‘QC.Rmd’ using ‘UTF-8’... OK ‘inferences.Rmd’ using ‘UTF-8’... OK ‘modeling.Rmd’ using ‘UTF-8’... OK ‘nonhuman.Rmd’ using ‘UTF-8’... OK ‘sesame.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK