############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings sesame_1.21.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’ * using R Under development (unstable) (2023-11-01 r85459) * 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 ‘1.21.0’ * 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 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 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 121.165 1.864 145.114 sesameQC_calcStats 31.019 0.196 32.354 sesameQC_plotHeatSNPs 26.739 0.156 28.032 KYCG_plotMeta 25.508 0.239 29.042 KYCG_plotEnrichAll 22.435 0.463 30.559 ELBAR 22.459 0.227 23.801 inferSpecies 20.350 0.581 24.242 matchDesign 20.206 0.112 21.452 sesameQC_plotBetaByDesign 17.920 0.084 18.037 compareMouseStrainReference 17.292 0.443 19.947 KYCG_annoProbes 15.615 0.292 19.202 testEnrichmentSEA 15.426 0.179 19.283 compareReference 14.819 0.307 17.325 diffRefSet 14.592 0.368 17.237 convertTo 14.389 0.391 16.997 sesameQC_plotBar 12.882 0.159 15.222 getRefSet 12.696 0.179 15.077 inferTissue 12.369 0.176 15.791 KYCG_plotMetaEnrichment 11.785 0.423 15.468 KYCG_buildGeneDBs 11.678 0.299 14.163 DMR 10.694 0.264 13.154 dbStats 10.635 0.227 13.080 getSexInfo 10.289 0.187 13.773 visualizeGene 10.332 0.124 13.731 inferStrain 10.190 0.256 12.618 KYCG_plotSetEnrichment 9.538 0.483 12.196 estimateLeukocyte 9.202 0.148 11.578 DML 8.879 0.311 11.675 sdf_read_table 8.439 0.148 10.782 createUCSCtrack 7.921 0.184 10.296 deidentify 7.825 0.151 10.157 dyeBiasNL 7.534 0.040 8.667 openSesame 7.046 0.100 9.339 inferSex 6.772 0.114 9.081 probeSuccessRate 6.508 0.103 11.582 reIdentify 6.470 0.064 7.629 scrubSoft 6.455 0.036 6.503 getMask 6.184 0.095 9.537 testEnrichment 6.031 0.168 9.443 dyeBiasCorrMostBalanced 6.103 0.084 8.381 prepSesame 5.487 0.055 6.615 bisConversionControl 5.095 0.168 7.436 KYCG_getDBs 5.065 0.096 7.349 sesameQC_rankStats 4.833 0.071 7.088 sesameQC_plotIntensVsBetas 4.707 0.056 5.855 visualizeProbes 4.529 0.068 5.688 inferSexKaryotypes 4.352 0.032 5.477 mapToMammal40 4.159 0.108 6.440 meanIntensity 3.497 0.064 5.720 dyeBiasCorr 3.402 0.128 5.704 totalIntensities 3.427 0.080 5.688 updateSigDF 3.314 0.084 5.574 print.DMLSummary 3.237 0.040 5.435 summaryExtractTest 3.039 0.072 5.284 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: OK