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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_1.15.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’
* using R version 4.2.1 Patched (2022-07-09 r82577)
* 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 ‘1.15.6’
* 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          29.414  1.654  34.512
KYCG_plotEnrichAll          26.646  1.018  28.881
sesameQC_plotHeatSNPs       25.514  1.546  27.247
inferSpecies                21.689  0.757  22.911
dyeBiasCorrMostBalanced     17.711  0.560  18.606
sesameQC_plotBar            14.937  0.792  15.951
getSexInfo                  14.838  0.700  15.945
KYCG_plotMeta               14.647  0.689  15.791
DMR                         14.777  0.450  15.471
diffRefSet                  13.710  0.625  14.546
probeSuccessRate            13.333  0.737  14.642
KYCG_plotMetaEnrichment     12.528  0.525  13.354
matchDesign                 12.504  0.522  13.194
sesameQC_plotBetaByDesign   11.040  1.133  12.201
inferStrain                 11.258  0.791  12.263
getRefSet                   11.448  0.523  12.167
compareMouseStrainReference 11.465  0.378  12.062
KYCG_annoProbes             11.321  0.451  11.988
dyeBiasCorr                 11.042  0.492  11.848
compareReference            10.108  0.549  10.839
KYCG_buildGeneDBs           10.164  0.404  10.757
testEnrichment               8.994  0.649   9.941
controls                     9.114  0.417   9.943
dbStats                      8.731  0.587   9.502
visualizeGene                8.831  0.481   9.646
detectionIB                  8.167  1.098   9.375
testEnrichmentSEA            8.436  0.723   9.658
inferSex                     7.909  0.521   8.610
prepSesame                   7.821  0.469   8.541
DML                          7.277  0.888   8.488
mapToMammal40                7.532  0.424   8.295
inferTissue                  6.707  1.249   8.204
formatVCF                    7.478  0.438   8.220
estimateLeukocyte            7.152  0.536   7.882
openSesame                   6.811  0.609   7.621
detectionPnegEcdf            7.025  0.357   7.555
dyeBiasNL                    6.390  0.469   6.980
noMasked                     5.996  0.143   6.393
KYCG_plotSetEnrichment       5.411  0.395   5.958
openSesameToFile             5.686  0.077   5.782
reIdentify                   5.212  0.396   5.703
bisConversionControl         5.364  0.210   5.733
createUCSCtrack              5.332  0.203   5.763
inferSexKaryotypes           5.218  0.276   5.586
sdf_read_table               5.139  0.244   5.504
deidentify                   5.113  0.237   5.526
scrubSoft                    4.576  0.545   5.143
* 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 Patched (2022-07-09 r82577) -- "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 
 30.467   1.738  32.803