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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_1.22.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.22.2’
* 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            174.643  7.950 216.705
imputeBetasByGenomicNeighbors  62.375  1.723  72.220
inferSex                       37.950  1.282  44.473
sesameQC_calcStats             35.614  2.320  43.745
KYCG_plotMeta                  34.077  1.186  40.852
compareMouseStrainReference    31.561  0.999  52.034
KYCG_plotEnrichAll             30.603  1.519  38.892
imputeBetas                    29.233  1.785  36.011
sesameQC_plotHeatSNPs          28.537  1.665  36.009
compareReference               28.823  0.821  35.857
KYCG_annoProbes                24.460  1.364  30.209
diffRefSet                     24.193  0.916  29.644
ELBAR                          22.275  2.689  29.139
matchDesign                    21.742  1.021  25.589
inferSpecies                   21.444  1.106  25.513
getRefSet                      19.568  0.680  22.944
sesameQC_plotBar               18.920  0.506  23.095
KYCG_plotMetaEnrichment        18.679  0.738  22.371
DML                            17.134  1.768  21.913
testEnrichmentSEA              16.992  1.144  22.081
sesameQC_plotBetaByDesign      16.130  1.547  21.137
sdf_read_table                 16.090  1.467  20.046
DMR                            16.508  0.469  20.102
KYCG_buildGeneDBs              16.247  0.722  20.071
visualizeGene                  15.776  0.616  19.863
inferStrain                    14.707  0.986  19.851
deidentify                     14.585  0.503  17.869
inferTissue                    11.593  1.743  15.208
reIdentify                     12.324  0.334  14.467
estimateLeukocyte              11.785  0.676  17.592
getMask                        11.291  0.726  14.459
openSesame                     10.322  1.194  13.309
dbStats                        10.356  0.802  13.386
KYCG_plotSetEnrichment          9.849  0.529  11.963
createUCSCtrack                 9.864  0.467  12.145
testEnrichment                  8.917  1.075  11.800
dyeBiasCorrMostBalanced         9.423  0.392  11.686
probeSuccessRate                8.799  0.801  11.314
updateSigDF                     8.657  0.635  11.628
dyeBiasNL                       8.165  0.510  10.256
sesameQC_rankStats              6.923  0.799   9.136
bisConversionControl            7.156  0.296   8.502
prepSesame                      6.802  0.527   9.010
noMasked                        5.869  0.339   7.290
scrubSoft                       5.138  0.957   6.944
sdf_write_table                 5.572  0.355   6.858
totalIntensities                5.145  0.399   7.137
summaryExtractTest              4.272  1.153   6.536
KYCG_plotWaterfall              5.124  0.250   6.215
print.DMLSummary                4.355  1.011   6.458
mapToMammal40                   4.861  0.477   6.116
detectionPnegEcdf               5.056  0.209   6.307
KYCG_getDBs                     4.871  0.374   6.633
parseGEOsignalMU                4.970  0.221   6.042
meanIntensity                   4.557  0.490   5.839
dyeBiasCorr                     4.639  0.317   5.973
checkLevels                     4.383  0.326   8.549
KYCG_plotPointRange             4.156  0.234   5.226
qualityMask                     3.812  0.545   5.087
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 36.189   3.520  46.119