############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sesame_1.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 (2024-04-24) * 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 ‘1.22.1’ * 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 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 101.152 10.176 114.660 imputeBetasByGenomicNeighbors 33.004 2.380 35.867 inferSex 22.673 2.064 25.058 KYCG_plotMeta 22.742 1.457 24.673 KYCG_plotEnrichAll 19.828 2.051 22.995 sesameQC_calcStats 18.837 1.256 20.250 imputeBetas 17.070 1.996 19.551 sesameQC_plotHeatSNPs 16.406 1.275 17.883 inferSpecies 15.188 1.984 17.683 ELBAR 15.590 1.020 16.776 KYCG_annoProbes 13.626 0.988 15.089 diffRefSet 12.397 0.824 13.537 KYCG_plotMetaEnrichment 12.054 1.132 13.665 sesameQC_plotBar 11.591 1.016 12.964 KYCG_buildGeneDBs 11.010 1.184 12.512 compareMouseStrainReference 11.147 0.957 12.420 compareReference 10.790 1.255 12.361 matchDesign 10.977 0.859 11.996 sesameQC_plotBetaByDesign 10.349 0.907 11.256 getRefSet 10.525 0.680 11.522 visualizeGene 9.618 0.517 10.648 testEnrichmentSEA 9.420 0.460 10.352 DMR 8.572 0.392 9.364 sdf_read_table 8.351 0.485 9.049 inferStrain 7.591 0.636 8.584 estimateLeukocyte 7.253 0.948 8.554 dyeBiasNL 7.225 0.832 8.218 inferTissue 7.172 0.731 8.222 getMask 6.870 0.728 8.419 DML 6.805 0.663 7.788 dbStats 6.200 0.980 7.495 KYCG_plotSetEnrichment 5.716 0.696 6.771 probeSuccessRate 5.481 0.664 6.617 dyeBiasCorrMostBalanced 5.597 0.384 6.296 createUCSCtrack 5.465 0.476 6.267 deidentify 5.378 0.504 6.199 testEnrichment 5.258 0.611 6.352 openSesame 4.827 0.620 5.770 bisConversionControl 4.656 0.424 5.461 reIdentify 4.278 0.667 5.104 * 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