############################################################################## ############################################################################## ### ### 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_1.26.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (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 ‘1.26.0’ * 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 imputeBetasByGenomicNeighbors 44.329 0.586 45.032 sesameQC_calcStats 29.600 0.180 29.857 inferSex 29.447 0.208 29.740 imputeBetas 27.012 0.306 27.494 sesameQC_plotHeatSNPs 24.983 0.730 25.770 ELBAR 22.362 0.159 22.579 sesameQC_plotBetaByDesign 20.383 0.786 21.230 inferSpecies 18.428 0.586 19.064 compareMouseStrainReference 17.510 0.151 17.710 matchDesign 16.859 0.120 17.035 diffRefSet 16.413 0.139 16.598 compareReference 15.546 0.156 15.745 getRefSet 13.184 0.198 13.417 sesameQC_plotBar 12.540 0.218 12.802 DMR 10.822 0.207 11.059 visualizeGene 10.088 0.391 10.510 inferStrain 10.047 0.347 10.430 DML 8.940 0.220 9.201 sdf_read_table 8.960 0.136 9.120 inferTissue 8.953 0.104 9.082 dyeBiasNL 8.052 0.039 8.121 deidentify 7.982 0.096 8.109 estimateLeukocyte 7.742 0.080 7.851 getMask 6.861 0.155 7.045 dyeBiasCorrMostBalanced 6.737 0.092 6.851 scrubSoft 6.558 0.064 6.636 openSesame 6.467 0.148 6.659 reIdentify 6.496 0.076 6.588 createUCSCtrack 6.201 0.171 6.392 probeSuccessRate 6.036 0.152 6.203 sesameQC_rankStats 5.614 0.171 5.801 prepSesame 5.224 0.080 5.320 * 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