############################################################################## ############################################################################## ### ### 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_1.25.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/sesame.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.25.3’ * 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 44.162 0.551 44.797 sesameQC_calcStats 28.945 0.247 29.241 imputeBetas 27.798 0.525 30.104 inferSex 27.727 0.208 27.991 sesameQC_plotHeatSNPs 24.141 0.147 24.328 ELBAR 21.540 0.195 21.769 inferSpecies 18.080 1.237 19.357 sesameQC_plotBetaByDesign 18.678 0.191 18.902 matchDesign 16.947 0.252 17.242 diffRefSet 16.784 0.163 16.997 compareMouseStrainReference 16.280 0.140 16.455 compareReference 14.736 0.195 14.956 getRefSet 12.853 0.159 13.072 sesameQC_plotBar 11.724 0.168 11.915 inferStrain 9.992 0.731 10.750 DMR 9.743 0.256 10.036 DML 9.670 0.319 10.013 visualizeGene 9.307 0.212 9.540 deidentify 9.087 0.104 9.224 sdf_read_table 8.897 0.128 9.043 inferTissue 8.550 0.431 8.999 estimateLeukocyte 8.413 0.164 8.611 dyeBiasNL 8.296 0.084 8.409 reIdentify 7.035 0.148 7.197 dyeBiasCorrMostBalanced 6.619 0.127 6.783 getMask 6.567 0.172 6.759 openSesame 6.479 0.176 6.692 scrubSoft 6.520 0.044 6.575 createUCSCtrack 6.094 0.096 6.206 probeSuccessRate 5.956 0.127 6.097 prepSesame 4.897 0.132 5.041 sesameQC_rankStats 4.917 0.092 5.021 * 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