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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_1.17.7.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.17.7’
* 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
KYCG_plotEnrichAll          44.697  0.980  64.081
sesameQC_calcStats          38.650  1.277  52.759
sesameQC_plotHeatSNPs       33.454  1.365  47.847
compareMouseStrainReference 29.301  0.504  40.738
inferSpecies                26.801  0.844  38.145
compareReference            25.900  0.653  36.868
matchDesign                 24.627  0.696  34.541
KYCG_plotMeta               23.243  0.599  33.463
ELBAR                       21.323  2.387  33.014
diffRefSet                  22.081  0.470  30.997
sesameQC_plotBetaByDesign   19.471  1.216  27.690
sesameQC_plotBar            19.903  0.477  27.655
KYCG_annoProbes             19.474  0.698  31.665
getRefSet                   17.939  0.402  25.335
KYCG_plotMetaEnrichment     16.450  0.416  23.617
KYCG_buildGeneDBs           16.324  0.450  24.486
DML                         15.390  1.048  22.727
DMR                         15.373  0.301  22.596
inferTissue                 14.715  0.800  28.075
visualizeGene               14.322  0.358  20.762
getSexInfo                  14.034  0.398  20.011
inferStrain                 13.566  0.741  19.692
testEnrichmentSEA           12.850  0.646  18.977
sdf_read_table              12.501  0.382  17.641
aggregateTestEnrichments    12.605  0.256  19.307
KYCG_plotSetEnrichment      11.909  0.409  17.980
deidentify                  11.715  0.172  22.830
dbStats                     10.548  0.587  15.522
estimateLeukocyte           10.302  0.425  20.706
reIdentify                  10.367  0.187  20.630
dyeBiasCorrMostBalanced      9.715  0.258  13.804
dyeBiasNL                    9.467  0.441  13.582
createUCSCtrack              9.289  0.279  13.513
probeSuccessRate             8.318  0.244  11.688
testEnrichment               7.952  0.342  11.608
openSesame                   7.413  0.597  12.826
inferSex                     7.558  0.404  10.915
visualizeProbes              7.572  0.134  10.850
bisConversionControl         7.414  0.180  10.626
sesameQC_rankStats           7.013  0.385  10.554
KYCG_plotPointRange          6.236  0.165   9.077
prepSesame                   5.872  0.117   8.167
updateSigDF                  5.631  0.261   8.353
scrubSoft                    5.309  0.568   7.929
parseGEOsignalMU             5.263  0.389   7.734
formatVCF                    5.363  0.274   7.840
checkLevels                  5.140  0.222   7.549
mapToMammal40                5.084  0.205   7.444
inferSexKaryotypes           5.015  0.213   7.205
KYCG_getDBs                  4.894  0.236   7.361
sdf_write_table              4.854  0.262   6.959
KYCG_plotWaterfall           4.752  0.162   6.838
detectionPnegEcdf            4.667  0.101   6.578
print.DMLSummary             4.223  0.542   6.655
dyeBiasCorr                  4.414  0.164   6.439
meanIntensity                4.321  0.136   6.258
sesameQC_plotIntensVsBetas   4.160  0.252  12.152
dyeBiasL                     4.216  0.158   6.035
totalIntensities             4.045  0.179   5.964
summaryExtractTest           3.703  0.511   5.982
sesame-package               3.632  0.373   5.770
scrub                        3.734  0.265   5.450
inferEthnicity               3.623  0.221   5.414
predictAge                   3.676  0.141   5.259
noMasked                     3.414  0.387   5.371
openSesameToFile             2.821  0.025   5.111
* 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:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL sesame
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3/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 Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences"
Copyright (C) 2023 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, 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 
 33.087   1.786  48.442