############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings sesame_1.16.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.16.1’ * 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 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 KYCG_plotEnrichAll 31.667 0.684 34.091 sesameQC_calcStats 23.017 0.168 23.440 sesameQC_plotHeatSNPs 21.677 0.260 22.193 KYCG_plotMeta 20.634 0.232 21.556 inferSpecies 17.031 0.800 18.421 DMR 16.724 0.376 17.781 diffRefSet 14.199 0.288 14.851 sesameQC_plotBetaByDesign 13.780 0.280 14.061 matchDesign 13.528 0.352 14.048 compareMouseStrainReference 13.032 0.176 13.648 KYCG_annoProbes 12.709 0.400 13.704 KYCG_plotMetaEnrichment 12.732 0.204 13.572 sesameQC_plotBar 12.047 0.236 12.796 compareReference 11.787 0.272 12.479 KYCG_buildGeneDBs 11.358 0.355 12.224 testEnrichment 11.068 0.296 12.396 getRefSet 10.710 0.152 11.289 testEnrichmentSEA 10.576 0.180 11.450 sdf_read_table 10.174 0.140 10.651 inferTissue 10.013 0.208 10.815 detectionIB 9.814 0.156 10.140 visualizeGene 9.529 0.268 10.392 getSexInfo 9.547 0.172 10.414 dbStats 8.611 0.304 9.423 DML 7.925 0.408 8.762 inferStrain 7.582 0.356 8.445 createUCSCtrack 7.505 0.200 8.123 estimateLeukocyte 7.164 0.144 7.833 dyeBiasNL 6.717 0.140 7.110 dyeBiasCorrMostBalanced 6.045 0.104 6.678 probeSuccessRate 5.983 0.132 6.895 deidentify 6.043 0.056 6.609 KYCG_plotSetEnrichment 5.836 0.088 6.460 openSesame 5.338 0.152 5.998 reIdentify 5.052 0.040 5.349 bisConversionControl 4.973 0.088 5.480 updateSigDF 4.642 0.152 5.216 * 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