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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 4.4.2 (2024-10-31)
* 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            65.861  4.048  70.853
imputeBetasByGenomicNeighbors 60.200  1.552  62.590
inferSex                      39.326  1.376  41.104
sesameQC_calcStats            35.010  2.758  38.602
KYCG_plotMeta                 32.345  1.089  34.066
sesameQC_plotHeatSNPs         30.754  1.702  33.066
compareMouseStrainReference   30.854  0.698  34.096
KYCG_plotEnrichAll            29.455  1.667  32.042
compareReference              28.322  1.076  30.296
imputeBetas                   25.627  1.806  28.035
ELBAR                         21.498  2.988  25.356
KYCG_annoProbes               23.373  1.107  25.035
diffRefSet                    23.448  0.952  24.820
matchDesign                   22.211  1.033  23.557
inferSpecies                  20.692  0.865  21.879
getRefSet                     19.615  0.712  20.663
sesameQC_plotBar              19.578  0.601  20.431
KYCG_plotMetaEnrichment       18.279  0.651  19.210
DML                           17.065  1.647  19.575
sesameQC_plotBetaByDesign     16.260  0.989  17.489
testEnrichmentSEA             15.848  1.289  17.633
KYCG_buildGeneDBs             16.288  0.605  17.349
sdf_read_table                15.949  0.649  17.046
visualizeGene                 15.681  0.753  16.555
DMR                           15.259  0.381  16.339
deidentify                    14.449  0.477  15.259
inferStrain                   13.441  0.821  14.416
reIdentify                    12.573  0.318  13.276
inferTissue                   11.221  1.379  12.763
dbStats                       10.728  0.846  11.777
dyeBiasNL                     10.582  0.591  11.341
estimateLeukocyte             10.425  0.683  11.460
getMask                       10.394  0.684  11.190
openSesame                     9.397  1.104  10.850
createUCSCtrack                9.705  0.489  10.671
KYCG_plotSetEnrichment         9.498  0.600  10.262
dyeBiasCorrMostBalanced        9.309  0.419   9.888
testEnrichment                 8.463  1.143   9.727
probeSuccessRate               8.626  0.860   9.561
bisConversionControl           7.162  0.298  22.188
noMasked                       6.117  0.686   6.932
visualizeProbes                6.591  0.097   6.727
prepSesame                     6.366  0.231   6.662
scrubSoft                      5.227  1.241   6.575
KYCG_plotWaterfall             6.047  0.349   6.640
sdf_write_table                5.868  0.304   6.224
sesameQC_rankStats             5.482  0.587   6.143
print.DMLSummary               4.721  1.289   6.079
updateSigDF                    5.424  0.425   5.906
parseGEOsignalMU               5.028  0.797   5.894
summaryExtractTest             4.180  1.160   5.863
detectionPnegEcdf              4.861  0.242   5.244
totalIntensities               4.666  0.419   5.232
dyeBiasCorr                    4.681  0.336   5.063
KYCG_getDBs                    4.629  0.371   5.271
* 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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, 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 
 36.482   2.845  40.343