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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings sesame_1.12.9.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.12.9’
* 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
cnSegmentation               48.559  2.263  51.509
visualizeSegments            48.646  1.919  51.397
DMR                          32.709  1.721  35.372
testEnrichment               26.260  1.636  28.923
bSubMostVariable             20.945  0.929  22.125
testEnrichmentGene           15.358  1.092  17.208
diffRefSet                   14.997  0.875  16.203
compareMouseTissueReference  14.674  1.004  16.099
compareMouseStrainReference  14.011  0.617  15.919
print.DMLSummary             12.095  1.068  13.577
visualizeGene                11.917  0.888  13.691
getProbesByChromosome        11.896  0.656  12.805
DML                          11.052  1.239  12.870
createUCSCtrack              11.202  0.652  12.286
getProbesByGene              11.001  0.816  12.247
as.data.frame.sesameQC       10.649  0.744  11.780
bSubProbes                   10.694  0.623  11.650
attachManifest               10.572  0.672  11.571
sdf_read_table               10.498  0.612  11.623
bisConversionControl         10.289  0.768  11.647
sesameQC                      9.891  1.032  11.088
inferTissue                   9.781  0.789  12.196
calcDatabaseSetStatisticsAll  9.577  0.954  19.695
getRefSet                     9.965  0.539  10.668
print.sesameQC                9.384  1.084  10.721
getDatabaseSetOverlap         9.407  0.744  10.692
deidentify                    9.210  0.713  10.427
dyeBiasCorrMostBalanced       8.878  0.600   9.904
reIdentify                    8.713  0.659   9.893
estimateLeukocyte             8.675  0.508   9.704
inferStrain                   8.242  0.797   9.632
dmContrasts                   8.444  0.540   9.359
summaryExtractTest            7.905  0.536   8.813
SNPcheck                      7.712  0.523   8.750
getProbesByRegion             6.712  0.619   7.497
bSubComplete                  6.395  0.604   7.269
qualityRank                   6.069  0.648   7.407
inferSex                      5.896  0.485   6.730
setMaskBySpecies              5.679  0.444   6.646
getNormCtls                   5.548  0.569   6.639
qualityMask                   5.329  0.386   6.222
getSexInfo                    4.956  0.681   5.802
dyeBiasCorrTypeINorm          4.742  0.536   5.442
getAutosomeProbes             4.763  0.256   5.274
SigDF                         4.521  0.400   5.257
dyeBiasCorr                   4.499  0.332   5.372
probeSuccessRate              4.477  0.303   5.288
predictMouseAgeInMonth        4.045  0.443   7.049
* 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-3.14-bioc/R/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
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 required package: rmarkdown
Loading sesameData.

----------------------------------------------------------
| SEnsible Step-wise Analysis of DNA MEthylation (SeSAMe)
| --------------------------------------------------------
| Please cache the annotation data for your array platform
| (e.g. EPIC) by calling "sesameDataCache("EPIC")"
| or "sesameDataCacheAll()". 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 
 17.299   1.273  19.005