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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            66.203  4.593  72.419
imputeBetasByGenomicNeighbors 58.996  1.538  61.459
sesameQC_calcStats            35.200  2.489  38.747
inferSex                      35.444  1.273  37.066
KYCG_plotMeta                 32.977  1.235  35.084
sesameQC_plotHeatSNPs         30.066  1.839  32.287
compareMouseStrainReference   30.325  0.682  36.276
KYCG_plotEnrichAll            29.167  1.559  31.369
compareReference              27.277  1.017  28.920
imputeBetas                   26.472  1.808  28.991
ELBAR                         21.753  3.259  25.273
KYCG_annoProbes               23.165  1.167  25.338
diffRefSet                    23.003  0.902  24.152
matchDesign                   22.061  0.979  23.440
inferSpecies                  20.113  0.935  21.590
sesameQC_plotBar              19.020  0.707  19.971
getRefSet                     18.644  0.785  19.798
KYCG_plotMetaEnrichment       18.389  0.767  19.429
DML                           16.968  1.647  19.623
sesameQC_plotBetaByDesign     16.431  1.060  17.786
testEnrichmentSEA             15.690  1.310  17.180
KYCG_buildGeneDBs             16.041  0.627  17.551
visualizeGene                 15.505  0.721  16.679
sdf_read_table                14.909  0.674  16.402
DMR                           15.174  0.402  16.161
deidentify                    14.330  0.501  15.238
inferStrain                   13.111  0.803  14.111
inferTissue                   11.622  1.533  13.341
reIdentify                    11.831  0.272  12.358
dbStats                       10.711  0.834  12.840
getMask                       10.394  0.649  11.293
estimateLeukocyte             10.382  0.645  11.380
dyeBiasNL                     10.335  0.561  11.019
openSesame                     9.518  1.164  10.837
KYCG_plotSetEnrichment         9.508  0.568  10.282
createUCSCtrack                9.340  0.476  11.321
testEnrichment                 8.395  1.188   9.894
dyeBiasCorrMostBalanced        9.136  0.370   9.690
probeSuccessRate               8.343  0.723   9.138
bisConversionControl           7.374  0.313  11.012
noMasked                       6.140  0.668   6.921
prepSesame                     6.384  0.247   6.743
KYCG_plotWaterfall             6.014  0.425   6.599
scrubSoft                      5.020  1.133   6.191
updateSigDF                    5.455  0.508   6.028
sesameQC_rankStats             5.385  0.421   6.036
print.DMLSummary               4.593  1.144   5.824
parseGEOsignalMU               5.020  0.687   5.857
summaryExtractTest             4.341  1.153   5.575
sdf_write_table                5.033  0.305   6.180
totalIntensities               4.753  0.383   5.238
detectionPnegEcdf              4.806  0.219   5.093
KYCG_getDBs                    4.621  0.390   5.062
visualizeProbes                4.763  0.105   5.021
checkLevels                    4.314  0.400  17.443
* 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 
 36.213   2.927  41.600