############################################################################## ############################################################################## ### ### 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_1.24.0.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 ‘1.24.0’ * 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 32.103 2.378 34.657 imputeBetasByGenomicNeighbors 24.162 0.943 25.162 KYCG_plotMeta 17.350 0.796 18.266 sesameQC_calcStats 16.791 1.347 18.188 inferSex 17.009 0.876 17.942 KYCG_plotEnrichAll 14.833 0.946 15.900 ELBAR 12.850 2.332 15.265 sesameQC_plotHeatSNPs 13.754 0.996 14.812 imputeBetas 12.930 1.003 13.992 KYCG_annoProbes 10.400 0.586 11.048 diffRefSet 10.024 0.451 10.503 inferSpecies 9.527 0.512 10.076 sesameQC_plotBar 9.657 0.231 9.911 sesameQC_plotBetaByDesign 8.688 1.142 9.865 KYCG_plotMetaEnrichment 9.135 0.448 9.662 compareMouseStrainReference 8.769 0.269 9.064 testEnrichmentSEA 8.006 0.882 8.954 matchDesign 8.309 0.567 8.930 getRefSet 8.179 0.401 8.619 KYCG_buildGeneDBs 8.216 0.331 8.593 visualizeGene 8.136 0.385 8.565 compareReference 7.601 0.428 8.051 DML 6.929 0.846 7.820 sdf_read_table 6.649 0.260 6.932 DMR 6.013 0.192 6.244 inferStrain 5.554 0.534 6.107 inferTissue 4.913 1.052 5.986 dbStats 5.230 0.459 5.712 dyeBiasNL 5.223 0.384 5.618 estimateLeukocyte 4.732 0.347 5.093 * 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