############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.23.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) 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 ‘1.23.9’ * 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 imputeBetasByGenomicNeighbors 45.872 0.538 46.524 testEnrichmentGene 44.996 0.775 45.862 inferSex 30.369 0.176 30.605 sesameQC_calcStats 29.703 0.084 29.842 imputeBetas 27.631 0.506 28.374 KYCG_plotMeta 26.151 0.188 26.390 sesameQC_plotHeatSNPs 25.490 0.167 25.710 ELBAR 21.926 0.363 22.333 KYCG_plotEnrichAll 20.759 0.443 21.253 sesameQC_plotBetaByDesign 19.195 0.095 19.329 inferSpecies 18.489 0.504 19.037 matchDesign 17.453 0.164 17.659 compareMouseStrainReference 16.728 0.159 16.927 compareReference 14.712 0.168 14.907 KYCG_annoProbes 14.600 0.271 14.908 diffRefSet 14.238 0.215 14.487 KYCG_plotMetaEnrichment 12.938 0.183 13.149 getRefSet 12.605 0.204 12.833 testEnrichmentSEA 12.640 0.147 12.809 sesameQC_plotBar 12.526 0.140 12.706 KYCG_buildGeneDBs 11.278 0.255 11.565 inferStrain 10.201 0.282 10.506 DML 9.736 0.279 10.046 DMR 9.723 0.215 9.963 visualizeGene 9.498 0.132 9.648 estimateLeukocyte 9.232 0.223 9.500 inferTissue 8.950 0.280 9.249 dbStats 8.767 0.191 9.001 dyeBiasNL 8.730 0.092 8.839 sdf_read_table 8.596 0.104 8.717 getMask 7.968 0.187 8.177 deidentify 7.498 0.072 7.593 KYCG_plotSetEnrichment 7.264 0.148 7.430 createUCSCtrack 6.921 0.128 7.068 openSesame 6.692 0.215 6.933 scrubSoft 6.557 0.008 6.576 probeSuccessRate 6.370 0.092 6.476 dyeBiasCorrMostBalanced 6.119 0.112 6.250 testEnrichment 6.060 0.148 6.220 reIdentify 6.003 0.040 6.055 sesameQC_rankStats 5.127 0.076 5.216 bisConversionControl 4.902 0.116 5.033 * 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