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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            185.016  8.439 227.090
imputeBetasByGenomicNeighbors  62.309  1.686  72.662
sesameQC_calcStats             36.696  2.078  45.194
inferSex                       36.640  1.283  42.465
KYCG_plotMeta                  35.690  1.199  43.524
sesameQC_plotHeatSNPs          34.497  2.097  42.191
compareMouseStrainReference    32.619  0.958  39.728
KYCG_plotEnrichAll             31.755  1.406  38.950
imputeBetas                    29.804  1.706  36.083
compareReference               29.338  0.821  35.263
ELBAR                          23.603  2.769  31.551
KYCG_annoProbes                25.002  1.345  32.089
diffRefSet                     24.154  1.056  34.738
matchDesign                    22.713  1.061  27.577
inferSpecies                   22.172  1.075  26.496
testEnrichmentSEA              19.935  1.313  25.680
sesameQC_plotBar               19.865  0.560  23.655
KYCG_plotMetaEnrichment        19.645  0.718  26.099
getRefSet                      19.099  0.684  22.968
DML                            17.783  1.849  23.696
sesameQC_plotBetaByDesign      17.015  1.261  21.975
DMR                            17.149  0.490  20.813
KYCG_buildGeneDBs              16.958  0.677  24.293
sdf_read_table                 16.287  0.783  20.213
visualizeGene                  16.389  0.640  20.252
inferStrain                    14.485  1.038  18.030
deidentify                     14.901  0.502  17.904
inferTissue                    12.290  1.543  16.189
reIdentify                     13.094  0.362  15.774
estimateLeukocyte              12.269  0.633  15.274
getMask                        11.698  0.739  15.128
dbStats                        10.789  0.864  13.811
createUCSCtrack                10.428  0.472  12.875
openSesame                     10.061  0.826  12.538
KYCG_plotSetEnrichment         10.183  0.576  12.827
probeSuccessRate                9.470  0.867  11.957
testEnrichment                  9.217  0.957  12.049
dyeBiasCorrMostBalanced         9.552  0.428  11.869
dyeBiasNL                       8.581  0.538  10.749
bisConversionControl            7.569  0.309   9.311
prepSesame                      7.209  0.462   9.516
scrubSoft                       5.427  1.450   7.949
sesameQC_rankStats              6.154  0.623   7.917
updateSigDF                     6.103  0.503   7.871
noMasked                        6.135  0.355   7.710
print.DMLSummary                4.648  1.160   6.987
parseGEOsignalMU                5.229  0.575   6.822
KYCG_plotWaterfall              5.515  0.270   7.568
sdf_write_table                 5.236  0.404   6.708
summaryExtractTest              4.492  1.056   6.365
meanIntensity                   4.864  0.598   6.458
mapToMammal40                   4.923  0.490   6.353
sesame-package                  4.722  0.673   6.279
KYCG_getDBs                     4.963  0.356   6.301
totalIntensities                4.993  0.292   6.390
detectionPnegEcdf               5.047  0.222   5.938
checkLevels                     4.766  0.327   6.057
dyeBiasCorr                     4.722  0.359   5.722
qualityMask                     4.155  0.608   5.624
KYCG_plotPointRange             4.445  0.256   5.641
dyeBiasL                        4.038  0.205   5.136
* 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:
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###   /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 
 38.475   3.026  47.117