############################################################################## ############################################################################## ### ### 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_1.24.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403) * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.24.0’ * 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 43.148 0.714 43.977 imputeBetasByGenomicNeighbors 40.559 0.495 41.144 inferSex 24.312 0.172 24.531 KYCG_plotMeta 23.384 0.139 23.589 imputeBetas 22.933 0.397 23.593 sesameQC_calcStats 22.601 0.124 22.790 sesameQC_plotHeatSNPs 20.282 0.171 20.507 KYCG_plotEnrichAll 19.552 0.475 20.103 inferSpecies 16.088 0.491 16.616 matchDesign 15.870 0.108 16.012 ELBAR 15.719 0.160 15.924 compareMouseStrainReference 15.688 0.076 15.818 KYCG_annoProbes 13.425 0.227 13.694 compareReference 13.444 0.192 13.673 sesameQC_plotBetaByDesign 13.278 0.096 13.420 diffRefSet 13.131 0.144 13.321 sesameQC_plotBar 12.062 0.163 12.263 KYCG_plotMetaEnrichment 11.924 0.220 12.178 testEnrichmentSEA 11.850 0.172 12.052 getRefSet 11.482 0.171 11.689 KYCG_buildGeneDBs 9.999 0.260 10.300 visualizeGene 9.531 0.171 9.722 DMR 9.163 0.203 9.398 DML 8.979 0.315 9.331 inferStrain 8.107 0.263 8.395 sdf_read_table 8.248 0.115 8.379 estimateLeukocyte 7.958 0.139 8.139 dbStats 7.810 0.120 7.960 inferTissue 7.283 0.307 7.611 KYCG_plotSetEnrichment 6.920 0.235 7.177 deidentify 6.733 0.095 6.859 getMask 6.553 0.147 6.729 dyeBiasNL 6.633 0.048 6.702 dyeBiasCorrMostBalanced 6.174 0.092 6.290 createUCSCtrack 6.127 0.095 6.245 openSesame 5.908 0.199 6.149 testEnrichment 5.517 0.096 5.630 probeSuccessRate 5.443 0.152 5.607 reIdentify 5.352 0.048 5.411 updateSigDF 5.261 0.104 5.378 bisConversionControl 5.046 0.087 5.153 * 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