############################################################################## ############################################################################## ### ### 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 4.4.3 (2025-02-28) * 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 ... 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 67.089 4.353 74.115 imputeBetasByGenomicNeighbors 60.638 1.600 63.324 inferSex 38.193 1.307 39.798 sesameQC_calcStats 34.736 2.038 37.361 KYCG_plotMeta 32.210 1.177 34.471 compareMouseStrainReference 30.680 0.578 32.992 sesameQC_plotHeatSNPs 29.091 1.507 31.154 KYCG_plotEnrichAll 28.713 1.768 31.034 compareReference 27.870 0.980 31.273 imputeBetas 26.435 1.850 28.737 ELBAR 22.924 3.421 26.859 diffRefSet 23.988 1.028 25.402 KYCG_annoProbes 23.255 1.164 25.471 matchDesign 21.885 1.120 23.280 inferSpecies 20.897 0.973 22.179 getRefSet 18.817 0.736 19.711 sesameQC_plotBar 19.059 0.485 19.861 sesameQC_plotBetaByDesign 17.348 1.549 19.075 DML 17.064 1.678 19.598 KYCG_plotMetaEnrichment 17.782 0.729 18.819 visualizeGene 17.395 0.841 18.542 testEnrichmentSEA 15.982 1.364 17.562 KYCG_buildGeneDBs 16.094 0.637 17.342 sdf_read_table 15.133 0.663 16.373 DMR 15.040 0.377 15.600 deidentify 14.203 0.538 15.049 inferStrain 12.920 0.695 13.835 inferTissue 11.085 1.453 12.743 reIdentify 11.990 0.313 12.442 dbStats 10.702 0.910 11.983 estimateLeukocyte 10.397 0.727 11.334 getMask 10.294 0.812 11.547 openSesame 9.357 0.907 10.395 KYCG_plotSetEnrichment 9.581 0.681 10.365 dyeBiasNL 9.314 0.538 9.918 createUCSCtrack 9.334 0.425 9.893 dyeBiasCorrMostBalanced 9.295 0.361 9.779 testEnrichment 8.480 1.014 10.040 probeSuccessRate 8.489 0.656 9.287 bisConversionControl 7.396 0.353 7.821 parseGEOsignalMU 5.606 1.184 6.903 noMasked 6.068 0.678 6.897 prepSesame 6.306 0.357 6.820 scrubSoft 5.150 1.239 6.530 updateSigDF 5.327 0.482 5.849 sesameQC_rankStats 5.394 0.368 5.987 sdf_write_table 5.158 0.308 5.722 print.DMLSummary 4.459 0.889 5.424 checkLevels 4.766 0.500 5.339 summaryExtractTest 4.030 1.080 5.350 detectionPnegEcdf 4.806 0.207 5.127 KYCG_plotWaterfall 4.732 0.272 5.044 totalIntensities 4.660 0.324 5.043 dyeBiasCorr 4.602 0.339 5.079 KYCG_getDBs 4.552 0.379 5.041 * 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