############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sesame_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.22.0’ * 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 124.283 1.794 147.918 inferSex 43.156 0.479 48.005 sesameQC_calcStats 30.170 0.195 31.491 KYCG_plotMeta 25.626 0.634 29.540 sesameQC_plotHeatSNPs 26.010 0.171 27.298 ELBAR 23.494 0.268 24.883 KYCG_plotEnrichAll 21.476 0.379 29.534 inferSpecies 19.458 0.543 23.253 matchDesign 17.937 0.319 19.364 sesameQC_plotBetaByDesign 17.514 0.120 17.664 compareMouseStrainReference 16.593 0.319 19.102 KYCG_annoProbes 16.330 0.352 20.140 diffRefSet 16.210 0.280 18.666 compareReference 15.070 0.276 17.512 KYCG_plotMetaEnrichment 13.404 0.434 17.097 sesameQC_plotBar 13.581 0.204 15.960 testEnrichmentSEA 12.610 0.196 16.253 getRefSet 12.576 0.176 14.911 KYCG_buildGeneDBs 12.003 0.291 14.466 visualizeGene 10.948 0.172 14.366 DMR 10.790 0.275 13.332 inferStrain 10.442 0.212 12.819 dyeBiasNL 9.910 0.104 11.100 dbStats 9.333 0.276 11.772 DML 8.791 0.458 11.625 inferTissue 8.745 0.252 11.182 sdf_read_table 8.789 0.128 11.074 estimateLeukocyte 7.987 0.196 10.355 KYCG_plotSetEnrichment 7.832 0.261 10.327 deidentify 7.538 0.148 9.887 openSesame 6.926 0.379 9.475 createUCSCtrack 6.946 0.139 9.271 probeSuccessRate 6.743 0.200 10.174 testEnrichment 6.487 0.191 9.910 scrubSoft 6.515 0.060 6.586 reIdentify 6.431 0.128 7.649 dyeBiasCorrMostBalanced 6.336 0.083 8.688 getMask 5.557 0.132 8.935 bisConversionControl 5.234 0.123 7.523 prepSesame 4.888 0.196 6.165 sesameQC_rankStats 4.986 0.080 7.234 print.DMLSummary 3.939 0.246 6.359 parseGEOsignalMU 3.835 0.156 5.067 mapToMammal40 3.922 0.068 6.149 checkLevels 3.770 0.200 5.054 dyeBiasCorr 3.729 0.072 6.055 qualityMask 3.692 0.108 5.953 totalIntensities 3.500 0.079 5.737 meanIntensity 3.369 0.087 5.631 summaryExtractTest 3.238 0.100 5.489 sesameQC_plotIntensVsBetas 3.281 0.036 6.852 updateSigDF 3.162 0.092 5.418 KYCG_getDBs 3.127 0.091 5.978 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK