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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings sesame_1.14.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/sesame.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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          33.119  1.039  34.422
KYCG_plotEnrichAll          29.643  3.163  34.323
DMR                         28.349  1.928  31.151
sesameQC_plotHeatSNPs       27.320  0.912  28.484
inferSpecies                21.652  2.044  24.447
DML                         21.770  1.120  23.313
dyeBiasCorrMostBalanced     17.578  1.289  19.538
KYCG_plotMeta               17.115  1.260  18.959
sesameQC_plotBar            15.536  0.800  16.843
getSexInfo                  14.852  1.024  16.717
matchDesign                 14.812  0.887  15.910
sesameQC_plotBetaByDesign   14.646  0.455  15.100
probeSuccessRate            13.446  1.112  15.477
diffRefSet                  13.295  1.060  14.699
KYCG_plotMetaEnrichment     12.934  1.137  14.760
KYCG_annoProbes             12.749  1.256  14.786
dyeBiasCorr                 12.587  1.055  14.497
prepSesame                  11.274  1.024  12.885
compareMouseTissueReference 11.459  0.836  12.625
KYCG_buildGeneDBs           10.752  1.164  12.248
compareMouseStrainReference 11.148  0.604  12.260
getRefSet                   10.707  0.692  11.814
testEnrichment              10.221  0.975  12.120
inferStrain                 10.064  0.868  11.452
visualizeGene                9.954  0.803  11.362
controls                     9.795  0.829  11.370
dbStats                      9.532  0.960  11.001
testEnrichmentGSEA           9.733  0.691  11.008
estimateLeukocyte            7.689  0.791   8.814
dyeBiasNL                    7.911  0.456   8.530
inferSex                     7.672  0.560   8.562
formatVCF                    7.531  0.645  10.439
detectionIB                  7.511  0.604   8.282
detectionPnegEcdf            7.316  0.588   8.335
inferTissue                  7.174  0.696   8.199
mapToMammal40                6.726  0.576   8.064
openSesame                   6.669  0.544   7.575
scrubSoft                    6.352  0.319   6.671
reIdentify                   6.004  0.628   6.797
noMasked                     5.895  0.539   6.764
createUCSCtrack              5.895  0.460   6.771
sdf_read_table               5.878  0.321   6.450
predictAgeHorvath353         5.454  0.663   6.453
deidentify                   5.445  0.428   6.384
sesame-package               5.359  0.476   5.999
bisConversionControl         5.282  0.532   6.145
print.DMLSummary             5.080  0.517   6.015
inferEthnicity               4.998  0.444   5.607
openSesameToFile             4.862  0.351   5.212
predictAgeSkinBlood          4.682  0.504   5.601
inferSexKaryotypes           4.650  0.353   5.170
summaryExtractTest           4.588  0.415   5.334
* 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:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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-pc-linux-gnu (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 
 31.026   2.352  34.291