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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_1.22.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.22.1’
* 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 code 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 whether 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
testEnrichmentGene            120.524  5.297 128.481
imputeBetasByGenomicNeighbors  39.766  1.490  41.655
KYCG_plotMeta                  25.276  0.915  26.503
inferSex                       24.058  1.230  25.576
sesameQC_calcStats             22.263  1.997  24.396
KYCG_plotEnrichAll             21.105  1.048  22.587
imputeBetas                    20.313  1.541  22.322
sesameQC_plotHeatSNPs          19.705  1.545  21.401
ELBAR                          17.021  3.182  20.388
KYCG_annoProbes                14.973  0.829  16.101
diffRefSet                     14.866  0.630  15.648
inferSpecies                   14.770  0.695  15.685
getRefSet                      13.188  0.554  13.888
sesameQC_plotBar               13.193  0.303  13.674
KYCG_plotMetaEnrichment        12.716  0.560  13.614
compareMouseStrainReference    12.617  0.493  13.238
sesameQC_plotBetaByDesign      10.908  1.565  12.531
matchDesign                    11.674  0.660  12.425
testEnrichmentSEA              11.370  0.928  12.693
KYCG_buildGeneDBs              11.740  0.491  12.385
compareReference               11.454  0.476  12.065
visualizeGene                  10.998  0.560  11.852
DML                             9.410  1.240  10.821
sdf_read_table                  9.450  1.066  10.664
inferStrain                     9.889  0.493  10.505
DMR                             9.449  0.277   9.857
inferTissue                     7.493  1.813   9.519
estimateLeukocyte               8.699  0.581   9.418
getMask                         7.714  0.615   8.608
dbStats                         7.074  0.743   8.037
openSesame                      6.415  1.165   7.723
testEnrichment                  6.285  0.816   7.520
createUCSCtrack                 6.578  0.400   7.452
KYCG_plotSetEnrichment          6.346  0.486   7.021
dyeBiasCorrMostBalanced         6.371  0.228   6.723
dyeBiasNL                       5.685  0.525   6.319
deidentify                      5.696  0.320   6.278
probeSuccessRate                5.602  0.387   6.203
bisConversionControl            5.138  0.242   5.498
reIdentify                      4.836  0.197   5.100
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/4.4-x86_64/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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, 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 5 ]
> 
> proc.time()
   user  system elapsed 
 23.085   1.831  25.321