############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings sesame_1.23.8.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: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.8’ * 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 64.950 1.375 68.550 imputeBetasByGenomicNeighbors 50.425 2.619 53.526 inferSex 32.314 1.104 33.866 sesameQC_calcStats 28.646 0.883 29.942 sesameQC_plotHeatSNPs 27.404 0.387 28.252 imputeBetas 24.796 1.120 26.453 inferSpecies 22.120 1.147 23.754 KYCG_plotMeta 22.293 0.244 22.912 diffRefSet 18.693 0.268 19.324 KYCG_plotEnrichAll 18.350 0.388 19.351 sesameQC_plotBar 17.272 0.424 17.949 matchDesign 16.310 1.060 17.645 getRefSet 16.669 0.199 17.254 ELBAR 16.491 0.371 17.023 testEnrichmentSEA 16.384 0.384 17.205 sesameQC_plotBetaByDesign 14.879 0.460 15.469 visualizeGene 14.280 0.309 15.146 sdf_read_table 14.233 0.335 15.092 KYCG_annoProbes 13.654 0.412 14.443 inferStrain 11.296 0.551 12.182 KYCG_plotMetaEnrichment 11.389 0.204 11.766 compareMouseStrainReference 11.116 0.136 11.469 compareReference 10.986 0.160 11.397 estimateLeukocyte 10.650 0.252 11.268 KYCG_buildGeneDBs 10.404 0.316 10.857 inferTissue 9.775 0.390 10.547 getMask 9.877 0.180 10.434 deidentify 9.268 0.132 9.742 dbStats 8.879 0.260 9.490 DMR 8.797 0.245 9.294 openSesame 8.338 0.645 9.481 probeSuccessRate 8.478 0.236 9.286 createUCSCtrack 8.486 0.116 8.994 testEnrichment 8.102 0.252 8.806 dyeBiasCorrMostBalanced 8.104 0.120 8.558 dyeBiasNL 7.941 0.100 8.242 DML 6.675 0.247 7.152 reIdentify 6.540 0.160 6.914 prepSesame 6.085 0.480 6.728 noMasked 5.619 0.292 6.292 sesameQC_rankStats 5.538 0.351 6.280 KYCG_plotSetEnrichment 5.633 0.168 6.022 updateSigDF 5.360 0.096 5.843 parseGEOsignalMU 5.075 0.320 5.714 scrubSoft 4.848 0.360 5.253 mapToMammal40 4.844 0.276 5.508 print.DMLSummary 4.507 0.540 5.351 meanIntensity 4.600 0.332 5.258 sdf_write_table 4.712 0.124 5.158 summaryExtractTest 4.544 0.240 5.025 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK