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### 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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.20.0’
* 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 R 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 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          126.297  5.667 134.786
sesameQC_calcStats           24.795  2.163  27.154
KYCG_plotMeta                24.229  1.060  25.632
KYCG_plotEnrichAll           20.514  1.062  22.164
sesameQC_plotHeatSNPs        19.894  1.551  21.816
ELBAR                        16.903  3.266  20.441
inferSpecies                 17.111  0.791  18.273
convertTo                    15.089  0.399  15.666
KYCG_annoProbes              14.351  0.875  15.501
testEnrichmentSEA            13.677  1.171  15.343
matchDesign                  13.833  0.824  14.802
sesameQC_plotBar             13.531  0.567  14.352
diffRefSet                   13.246  0.572  14.054
compareMouseStrainReference  13.343  0.410  13.987
sesameQC_plotBetaByDesign    11.814  1.619  13.504
getRefSet                    12.737  0.613  13.511
inferTissue                  10.851  1.554  12.869
compareReference             11.668  0.647  12.588
KYCG_plotMetaEnrichment      11.266  0.608  12.144
KYCG_buildGeneDBs            11.281  0.485  11.989
visualizeGene                10.555  0.547  11.448
getSexInfo                    9.877  0.633  10.904
DML                           8.953  1.355  10.799
DMR                           9.500  0.386  10.174
sdf_read_table                9.159  0.423   9.758
inferStrain                   8.471  0.758   9.403
estimateLeukocyte             8.135  0.598   8.886
dbStats                       7.246  0.747   8.144
createUCSCtrack               7.501  0.327   7.971
dyeBiasNL                     6.862  0.609   7.605
dyeBiasCorrMostBalanced       6.995  0.302   7.490
testEnrichment                6.233  0.846   7.269
KYCG_plotSetEnrichment        6.391  0.623   7.185
openSesame                    5.753  1.149   7.044
probeSuccessRate              6.416  0.469   7.188
deidentify                    6.382  0.363   6.993
getMask                       5.727  0.411   6.328
bisConversionControl          5.558  0.273   6.164
inferSex                      5.060  0.482   5.673
reIdentify                    5.148  0.375   5.620
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘sesame’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (sesame)

R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(sesame)
Loading required package: sesameData
Loading required package: ExperimentHub
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache auxiliary data by "sesameDataCache()".
| This needs to be done only once per SeSAMe installation.
----------------------------------------------------------

> 
> test_check("sesame")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
 22.764   1.907  24.902