############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:sesame.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings sesame_1.23.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘sesame/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘sesame’ version ‘1.23.9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' 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 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 32.351 2.331 34.805 imputeBetasByGenomicNeighbors 24.073 1.005 25.107 inferSex 17.356 0.733 18.108 sesameQC_calcStats 16.821 1.105 17.951 KYCG_plotMeta 16.034 0.768 16.855 ELBAR 13.494 2.362 15.890 KYCG_plotEnrichAll 14.447 1.009 15.535 sesameQC_plotHeatSNPs 13.159 0.889 14.073 imputeBetas 12.727 1.035 13.780 inferSpecies 10.967 0.502 11.481 sesameQC_plotBar 9.886 0.253 10.153 KYCG_annoProbes 9.481 0.598 10.106 diffRefSet 9.067 0.569 9.651 KYCG_plotMetaEnrichment 8.692 0.546 9.262 sesameQC_plotBetaByDesign 8.301 0.873 9.182 compareMouseStrainReference 8.618 0.413 9.049 matchDesign 8.073 0.630 8.728 testEnrichmentSEA 7.729 0.904 8.653 KYCG_buildGeneDBs 8.077 0.393 8.493 getRefSet 8.105 0.346 8.464 compareReference 8.036 0.406 8.457 DML 6.845 0.860 7.734 visualizeGene 7.198 0.404 7.618 sdf_read_table 6.294 0.262 6.573 estimateLeukocyte 5.473 0.430 5.911 DMR 5.708 0.193 5.912 inferStrain 5.315 0.441 5.764 inferTissue 4.836 0.898 5.740 dyeBiasNL 5.272 0.376 5.653 dbStats 4.876 0.555 5.446 getMask 4.621 0.606 5.237 * 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