############################################################################## ############################################################################## ### ### 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 43.891 0.841 44.889 imputeBetasByGenomicNeighbors 41.436 0.531 42.081 inferSex 25.127 0.207 25.403 sesameQC_calcStats 23.639 0.140 23.841 KYCG_plotMeta 23.352 0.140 23.560 imputeBetas 22.833 0.335 23.409 sesameQC_plotHeatSNPs 21.761 0.140 21.963 KYCG_plotEnrichAll 19.030 0.506 19.606 inferSpecies 16.350 0.359 16.757 matchDesign 16.151 0.171 16.362 ELBAR 15.959 0.240 16.252 compareMouseStrainReference 15.500 0.084 15.622 sesameQC_plotBetaByDesign 13.593 0.076 13.704 compareReference 13.437 0.211 13.679 KYCG_annoProbes 13.266 0.179 13.490 diffRefSet 12.650 0.203 12.889 sesameQC_plotBar 12.250 0.151 12.437 testEnrichmentSEA 12.075 0.144 12.256 KYCG_plotMetaEnrichment 11.673 0.215 11.924 getRefSet 11.358 0.131 11.516 visualizeGene 9.880 0.172 10.082 KYCG_buildGeneDBs 9.779 0.247 10.059 DML 8.924 0.315 9.274 DMR 9.034 0.155 9.220 inferStrain 8.442 0.263 8.736 sdf_read_table 8.412 0.095 8.532 inferTissue 7.702 0.227 7.953 estimateLeukocyte 7.693 0.195 7.926 dbStats 7.334 0.139 7.505 KYCG_plotSetEnrichment 6.891 0.128 7.045 deidentify 6.796 0.064 6.887 openSesame 6.461 0.211 6.717 dyeBiasNL 6.626 0.040 6.685 getMask 6.476 0.136 6.633 dyeBiasCorrMostBalanced 6.016 0.076 6.107 createUCSCtrack 5.926 0.108 6.050 probeSuccessRate 5.656 0.108 5.779 testEnrichment 5.655 0.104 5.776 updateSigDF 5.504 0.108 5.631 reIdentify 5.533 0.008 5.552 * 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