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### Running command:
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###   /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_1.14.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.14.2’
* 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 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
sesameQC_calcStats          56.757  2.370  59.478
sesameQC_plotHeatSNPs       46.912  1.824  48.998
DMR                         46.019  0.617  47.830
KYCG_plotEnrichAll          37.844  0.903  40.580
inferSpecies                33.888  0.847  35.626
DML                         33.695  0.836  35.098
dyeBiasCorrMostBalanced     27.956  0.462  29.054
sesameQC_plotBetaByDesign   25.666  1.360  27.065
compareMouseStrainReference 26.144  0.317  26.861
sesameQC_plotBar            24.361  0.602  25.337
KYCG_plotMeta               23.570  0.657  25.019
matchDesign                 23.248  0.704  24.302
compareMouseTissueReference 23.057  0.421  23.983
diffRefSet                  22.337  0.661  23.613
getSexInfo                  20.566  0.504  21.949
detectionIB                 18.862  1.758  20.821
KYCG_annoProbes             19.192  0.694  20.616
probeSuccessRate            19.171  0.479  20.941
KYCG_plotMetaEnrichment     18.885  0.498  20.301
inferStrain                 18.469  0.692  19.616
getRefSet                   17.663  0.430  18.578
prepSesame                  17.352  0.679  18.843
dyeBiasCorr                 16.507  0.467  17.839
KYCG_buildGeneDBs           15.675  0.434  16.554
visualizeGene               15.098  0.337  16.230
testEnrichmentGSEA          14.567  0.727  16.049
controls                    14.272  0.435  15.541
testEnrichment              13.971  0.455  15.432
dbStats                     12.098  0.731  13.391
inferTissue                 11.792  0.731  12.973
deidentify                  12.023  0.234  12.703
inferSex                    11.266  0.357  12.160
detectionPnegEcdf           11.223  0.293  11.947
formatVCF                   11.112  0.366  20.236
mapToMammal40               10.672  0.268  11.551
reIdentify                  10.752  0.171  11.139
dyeBiasNL                   10.478  0.400  11.147
openSesame                  10.603  0.256  11.262
estimateLeukocyte           10.406  0.440  11.219
scrubSoft                   10.092  0.710  10.811
sdf_read_table              10.139  0.409  10.741
noMasked                     9.288  0.528  10.319
openSesameToFile             9.063  0.424   9.502
createUCSCtrack              8.894  0.221   9.593
scrub                        8.509  0.425   8.950
inferSexKaryotypes           8.563  0.255   9.141
print.DMLSummary             7.969  0.374   8.936
bisConversionControl         7.800  0.179   8.317
predictAgeHorvath353         7.347  0.578   8.401
inferEthnicity               7.613  0.297   8.088
visualizeProbes              7.603  0.207   8.073
summaryExtractTest           7.122  0.572   8.242
noob                         6.591  0.570   7.198
predictAgeSkinBlood          6.603  0.352   7.511
sesameQC_rankStats           6.181  0.455   7.200
sesameQC_getStats            6.371  0.242   6.630
qualityMask                  6.109  0.193   6.528
KYCG_getDBs                  5.745  0.216   6.444
predictMouseAgeInMonth       5.603  0.226   6.395
KYCG_plotPointRange          5.577  0.153   6.010
updateSigDF                  5.187  0.229   5.912
sesameQC_plotIntensVsBetas   5.038  0.347   5.557
sesame-package               5.135  0.172   5.566
pOOBAH                       4.910  0.288   5.203
checkLevels                  4.855  0.230   5.260
totalIntensities             4.669  0.224   5.372
KYCG_plotWaterfall           4.737  0.138   5.193
meanIntensity                4.420  0.362   5.245
* 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/4.2/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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, 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 
 48.394   2.129  51.290