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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_1.23.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.23.6’
* 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            73.294  4.330  83.506
imputeBetasByGenomicNeighbors 62.327  1.588  71.951
inferSex                      38.345  1.220  43.061
sesameQC_calcStats            36.948  1.973  42.620
KYCG_plotMeta                 36.327  1.116  40.590
sesameQC_plotHeatSNPs         32.085  1.977  37.663
KYCG_plotEnrichAll            32.089  1.442  41.372
compareMouseStrainReference   32.177  0.913  36.571
imputeBetas                   29.700  1.737  35.822
compareReference              29.335  0.771  33.112
KYCG_annoProbes               25.009  1.311  29.449
ELBAR                         23.523  2.746  28.983
diffRefSet                    24.932  0.879  28.634
matchDesign                   22.534  1.110  25.584
inferSpecies                  21.270  1.002  24.522
KYCG_plotMetaEnrichment       19.689  0.701  22.759
sesameQC_plotBar              19.715  0.565  25.754
getRefSet                     19.495  0.675  22.965
testEnrichmentSEA             18.401  1.225  21.612
DML                           17.247  1.754  21.505
visualizeGene                 17.382  0.734  21.436
DMR                           17.288  0.443  19.774
KYCG_buildGeneDBs             17.075  0.646  19.980
sdf_read_table                16.723  0.718  19.384
sesameQC_plotBetaByDesign     15.261  1.204  16.946
deidentify                    14.890  0.457  17.106
inferStrain                   13.861  0.858  16.471
inferTissue                   12.868  1.396  15.630
estimateLeukocyte             12.317  0.631  14.841
reIdentify                    12.623  0.325  13.894
getMask                       11.614  0.750  14.213
dbStats                       10.645  0.917  13.021
KYCG_plotSetEnrichment        10.388  0.533  12.405
createUCSCtrack               10.328  0.442  11.932
probeSuccessRate               9.622  0.768  11.768
openSesame                     9.605  0.705  11.118
testEnrichment                 9.218  0.995  11.174
dyeBiasCorrMostBalanced        9.787  0.365  11.413
dyeBiasNL                      8.707  0.534  10.091
totalIntensities               7.892  0.584   9.599
bisConversionControl           7.627  0.278   8.734
prepSesame                     7.199  0.459   8.607
scrubSoft                      5.346  1.267   7.171
sesameQC_rankStats             5.917  0.579   8.434
noMasked                       6.038  0.303   7.215
sdf_write_table                5.753  0.326   6.734
KYCG_plotWaterfall             5.605  0.235   6.423
parseGEOsignalMU               5.247  0.527   6.327
mapToMammal40                  5.149  0.544   6.325
updateSigDF                    5.233  0.399   6.509
print.DMLSummary               4.500  1.097   6.186
KYCG_getDBs                    4.951  0.366   5.942
summaryExtractTest             4.444  0.869   5.957
meanIntensity                  4.693  0.608   6.110
detectionPnegEcdf              5.101  0.189   5.826
dyeBiasCorr                    4.888  0.298   5.848
sesame-package                 4.555  0.593   5.733
checkLevels                    4.653  0.315   5.432
KYCG_plotPointRange            4.466  0.235   5.276
qualityMask                    4.150  0.540   5.547
formatVCF                      3.796  0.364   5.204
* 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 Patched (2024-04-24 r86482) -- "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 
 38.200   2.939  46.623