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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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.3 (2025-02-28)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.24.0’
* 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            65.966  4.716  71.362
imputeBetasByGenomicNeighbors 59.395  1.671  61.498
inferSex                      37.362  1.385  39.107
sesameQC_calcStats            35.299  2.021  37.917
KYCG_plotMeta                 32.724  1.141  34.185
compareMouseStrainReference   31.039  0.617  33.131
KYCG_plotEnrichAll            28.589  1.702  30.870
sesameQC_plotHeatSNPs         28.539  1.434  31.404
imputeBetas                   27.077  2.002  29.932
compareReference              28.040  0.988  29.597
ELBAR                         22.816  3.722  27.055
diffRefSet                    23.827  0.930  25.281
KYCG_annoProbes               23.487  1.156  25.533
matchDesign                   21.440  1.066  22.706
inferSpecies                  19.210  1.003  20.653
sesameQC_plotBar              19.197  0.523  19.915
getRefSet                     18.612  0.736  19.612
KYCG_plotMetaEnrichment       18.536  0.757  19.617
DML                           17.165  1.687  19.818
sesameQC_plotBetaByDesign     17.169  1.531  19.040
visualizeGene                 17.150  0.832  18.209
testEnrichmentSEA             16.080  1.227  17.558
KYCG_buildGeneDBs             16.070  0.702  17.918
sdf_read_table                15.898  0.688  16.960
DMR                           15.119  0.404  15.658
deidentify                    14.210  0.537  14.852
inferStrain                   12.315  0.690  13.127
reIdentify                    11.820  0.287  12.417
inferTissue                   10.602  1.400  12.112
dbStats                       10.926  0.879  12.092
dyeBiasNL                     10.781  0.726  11.592
getMask                       10.489  0.829  11.575
estimateLeukocyte             10.478  0.706  11.347
openSesame                     9.462  1.096  10.728
KYCG_plotSetEnrichment         9.763  0.652  10.525
createUCSCtrack                9.544  0.488  10.218
dyeBiasCorrMostBalanced        9.254  0.416   9.739
testEnrichment                 8.435  1.016   9.579
probeSuccessRate               8.508  0.674   9.271
bisConversionControl           7.386  0.322   8.750
noMasked                       6.030  0.687   7.156
scrubSoft                      5.133  1.246   6.855
parseGEOsignalMU               5.360  1.012   6.483
prepSesame                     6.038  0.321   6.410
sdf_write_table                5.845  0.315   6.304
updateSigDF                    5.505  0.489   6.067
sesameQC_rankStats             5.390  0.333   6.071
print.DMLSummary               4.459  1.055   5.584
summaryExtractTest             4.252  1.031   5.342
checkLevels                    4.787  0.478   6.171
detectionPnegEcdf              4.979  0.210   5.230
KYCG_plotWaterfall             4.875  0.229   5.129
totalIntensities               4.696  0.356   5.141
KYCG_getDBs                    4.556  0.401   5.091
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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, saveRDS, 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 
 36.209   2.886  40.794