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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_1.12.9.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/sesame.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.12.9’
* 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
visualizeSegments            84.244  2.635  88.136
cnSegmentation               82.960  3.445  87.458
DMR                          46.795  0.734  49.034
bSubMostVariable             38.915  0.487  39.689
testEnrichment               36.664  1.700  40.178
compareMouseTissueReference  28.937  0.532  30.093
compareMouseStrainReference  25.685  0.340  27.484
diffRefSet                   23.631  0.386  24.553
testEnrichmentGene           23.043  0.942  25.017
visualizeGene                18.587  0.444  20.099
createUCSCtrack              18.564  0.228  19.402
DML                          17.419  0.978  19.529
deidentify                   17.430  0.346  18.350
getProbesByChromosome        17.020  0.199  17.584
print.sesameQC               15.819  1.207  17.354
bSubProbes                   16.655  0.332  17.512
reIdentify                   16.107  0.633  17.502
sdf_read_table               15.943  0.671  17.177
attachManifest               15.979  0.354  16.970
print.DMLSummary             16.081  0.139  16.907
getProbesByGene              15.923  0.187  16.743
as.data.frame.sesameQC       14.545  1.182  16.002
getRefSet                    14.862  0.121  15.238
dmContrasts                  14.593  0.290  15.188
summaryExtractTest           14.496  0.146  15.178
getDatabaseSetOverlap        14.341  0.284  15.507
bisConversionControl         14.195  0.265  15.488
calcDatabaseSetStatisticsAll 13.442  0.713  16.286
inferTissue                  13.533  0.426  15.710
estimateLeukocyte            13.416  0.407  14.349
sesameQC                     12.088  1.203  13.571
inferStrain                  12.876  0.408  14.269
inferSex                     12.008  0.321  12.958
dyeBiasCorrMostBalanced      11.476  0.302  12.408
SNPcheck                     11.263  0.369  12.313
getProbesByRegion             8.809  0.099   9.176
setMaskBySpecies              8.609  0.152   9.351
qualityMask                   8.316  0.231   9.245
getNormCtls                   8.293  0.167   9.116
getAutosomeProbes             8.239  0.097   8.592
qualityRank                   8.123  0.158   9.185
dyeBiasCorr                   6.613  0.185   7.549
totalIntensities              6.465  0.197   7.286
controls                      6.131  0.168   7.007
probeSuccessRate              6.049  0.238   6.862
bSubComplete                  6.158  0.111   6.544
SigDF                         6.075  0.142   6.883
getSexInfo                    5.119  0.231   5.737
predictMouseAgeInMonth        5.172  0.153   7.107
getAFTypeIbySumAlleles        5.155  0.159   5.840
setMask                       5.027  0.205   5.496
sdf_write_table               4.971  0.212   5.565
dyeBiasCorrTypeINorm          4.739  0.327   5.342
createDatabaseSetNetwork      4.866  0.076   5.204
predictAgeHorvath353          4.829  0.096   5.336
compareDatbaseSetOverlap      4.656  0.099   5.014
formatVCF                     3.057  0.082   5.280
* 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/4.1/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 4.1.3 (2022-03-10) -- "One Push-Up"
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 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 
 25.210   1.556  27.523