############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings sesame_1.19.10.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’ * using R version 4.3.1 (2023-06-16) * using platform: aarch64-unknown-linux-gnu (64-bit) * 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 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.19.10’ * 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 128.352 4.393 155.183 sesameQC_calcStats 31.012 2.779 35.280 sesameQC_plotHeatSNPs 27.894 1.740 30.971 KYCG_plotMeta 24.311 1.325 29.215 KYCG_plotEnrichAll 22.427 1.856 32.358 ELBAR 22.203 0.942 24.306 matchDesign 20.962 0.522 22.638 inferSpecies 19.014 1.828 24.291 sesameQC_plotBetaByDesign 18.425 0.941 19.424 compareMouseStrainReference 17.339 0.922 20.524 compareReference 16.065 1.050 19.353 testEnrichmentSEA 15.955 0.543 19.858 KYCG_annoProbes 15.211 1.066 19.642 diffRefSet 14.707 1.018 19.710 convertTo 14.340 0.957 17.706 sesameQC_plotBar 13.786 0.614 16.794 getRefSet 13.360 0.871 16.544 inferTissue 12.608 0.997 17.068 KYCG_plotMetaEnrichment 11.604 0.801 16.878 DMR 11.368 0.662 14.391 KYCG_buildGeneDBs 11.136 0.881 16.448 visualizeGene 11.271 0.259 14.826 inferStrain 10.317 0.718 13.464 getSexInfo 9.967 0.688 14.677 KYCG_plotSetEnrichment 9.261 0.870 12.476 dbStats 8.965 1.046 12.478 sdf_read_table 8.898 1.022 12.275 DML 9.166 0.614 12.150 dyeBiasNL 8.588 0.586 10.292 createUCSCtrack 8.219 0.650 11.268 deidentify 8.002 0.546 10.792 estimateLeukocyte 7.794 0.520 10.602 openSesame 6.805 0.977 10.034 testEnrichment 6.674 1.037 11.069 reIdentify 6.710 0.558 8.842 dyeBiasCorrMostBalanced 6.803 0.384 9.504 probeSuccessRate 6.671 0.318 10.422 scrubSoft 6.586 0.319 6.919 inferSex 5.782 0.415 8.404 inferSexKaryotypes 5.464 0.663 7.253 getMask 5.523 0.538 9.390 sesameQC_rankStats 5.511 0.312 8.200 prepSesame 5.387 0.303 6.918 bisConversionControl 4.681 0.239 7.209 visualizeProbes 4.784 0.052 5.962 parseGEOsignalMU 4.072 0.351 5.547 mapToMammal40 4.011 0.303 6.634 qualityMask 3.735 0.252 6.207 sesame-package 3.356 0.562 5.030 checkLevels 3.531 0.347 5.103 summaryExtractTest 3.626 0.234 6.098 meanIntensity 3.470 0.319 6.415 dyeBiasCorr 3.502 0.195 5.920 print.DMLSummary 3.294 0.395 6.115 totalIntensities 3.416 0.096 5.997 updateSigDF 3.259 0.144 5.629 KYCG_getDBs 3.106 0.280 5.711 getAFTypeIbySumAlleles 2.236 0.164 5.013 * 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