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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 4.4.0 (2024-04-24)
* 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 ‘1.22.2’
* 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            183.999  8.294 234.023
imputeBetasByGenomicNeighbors  62.185  1.818  74.817
inferSex                       37.823  1.284  45.427
sesameQC_calcStats             36.785  1.572  44.279
KYCG_plotMeta                  35.649  1.087  41.921
sesameQC_plotHeatSNPs          32.641  1.707  37.983
compareMouseStrainReference    32.748  0.963  38.793
KYCG_plotEnrichAll             31.898  1.392  40.607
compareReference               29.525  0.798  34.393
imputeBetas                    27.448  1.798  35.020
KYCG_annoProbes                25.083  1.360  32.035
ELBAR                          23.361  2.803  31.260
diffRefSet                     24.538  0.867  29.025
inferSpecies                   21.932  1.117  26.793
matchDesign                    21.722  1.132  26.604
visualizeGene                  19.790  0.849  24.262
sesameQC_plotBar               19.868  0.608  24.056
KYCG_plotMetaEnrichment        19.646  0.705  25.271
getRefSet                      18.984  0.637  23.140
DML                            17.799  1.801  23.512
testEnrichmentSEA              17.736  1.037  22.696
sesameQC_plotBetaByDesign      17.103  1.324  21.871
DMR                            17.297  0.467  20.766
KYCG_buildGeneDBs              16.980  0.686  21.277
sdf_read_table                 16.896  0.757  20.955
deidentify                     14.649  0.455  17.326
inferStrain                    13.494  0.925  16.931
reIdentify                     12.681  0.317  15.203
inferTissue                    11.593  1.397  15.347
estimateLeukocyte              12.117  0.655  15.142
getMask                        11.668  0.769  14.931
dbStats                        10.684  0.852  13.290
openSesame                      9.992  1.002  13.138
KYCG_plotSetEnrichment         10.420  0.547  13.119
createUCSCtrack                10.489  0.458  12.430
dyeBiasNL                      10.115  0.611  12.532
testEnrichment                  9.316  0.971  11.521
probeSuccessRate                9.441  0.686  12.132
dyeBiasCorrMostBalanced         9.676  0.399  11.888
bisConversionControl            7.596  0.315   9.140
prepSesame                      7.009  0.545   8.844
meanIntensity                   5.871  1.011  10.640
noMasked                        6.249  0.343   8.114
sdf_write_table                 6.106  0.365   7.487
updateSigDF                     5.797  0.433   7.564
sesameQC_rankStats              5.634  0.481   6.945
scrubSoft                       5.322  0.692   6.946
totalIntensities                5.542  0.351   7.276
parseGEOsignalMU                5.221  0.563   6.972
KYCG_plotWaterfall              5.456  0.245   6.502
summaryExtractTest              4.716  0.869   6.163
KYCG_getDBs                     5.013  0.358   6.707
mapToMammal40                   4.912  0.455   6.381
sesameQC_getStats               4.622  0.643   6.034
detectionPnegEcdf               5.052  0.189   5.925
dyeBiasCorr                     4.870  0.332   6.153
sesame-package                  4.715  0.428   6.028
checkLevels                     4.725  0.343   5.834
print.DMLSummary                4.324  0.630   5.976
qualityMask                     4.215  0.518   5.479
KYCG_plotPointRange             4.414  0.223   5.382
scrub                           3.829  0.520   5.207
predictAge                      4.076  0.197   5.021
formatVCF                       3.795  0.333   5.093
* 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 (2024-04-24) -- "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 
 38.441   3.107  48.489