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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_1.23.5.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 ‘1.23.5’
* 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            74.486  4.336  85.326
imputeBetasByGenomicNeighbors 63.014  1.647  72.174
inferSex                      38.644  1.270  45.248
sesameQC_calcStats            36.277  1.770  40.914
KYCG_plotMeta                 36.901  1.063  40.492
compareMouseStrainReference   32.634  0.869  39.160
KYCG_plotEnrichAll            31.203  1.346  35.985
sesameQC_plotHeatSNPs         30.781  1.303  35.812
compareReference              29.529  0.897  34.452
imputeBetas                   27.876  1.802  33.552
KYCG_annoProbes               25.449  1.309  29.020
ELBAR                         23.345  2.691  29.106
diffRefSet                    24.880  0.950  29.456
matchDesign                   22.471  0.917  25.295
sesameQC_plotBar              21.467  0.826  24.772
inferSpecies                  20.899  1.023  24.892
KYCG_plotMetaEnrichment       20.655  0.756  23.348
getRefSet                     19.339  0.541  22.385
testEnrichmentSEA             17.952  1.304  20.996
DML                           17.151  1.708  21.076
visualizeGene                 17.566  0.771  20.539
KYCG_buildGeneDBs             17.247  0.653  19.426
sdf_read_table                16.732  0.692  19.612
DMR                           16.860  0.426  18.751
sesameQC_plotBetaByDesign     15.497  1.192  17.691
deidentify                    14.834  0.508  17.952
inferStrain                   13.823  0.863  16.312
inferTissue                   12.874  1.538  15.563
dbStats                       12.017  0.971  15.136
reIdentify                    12.570  0.272  13.947
getMask                       11.766  0.740  14.495
dyeBiasNL                     11.090  0.587  12.777
estimateLeukocyte             10.877  0.598  12.899
KYCG_plotSetEnrichment        10.522  0.557  12.154
createUCSCtrack               10.355  0.454  12.664
testEnrichment                 9.491  0.919  11.145
probeSuccessRate               9.645  0.746  11.702
openSesame                     9.669  0.641  11.300
dyeBiasCorrMostBalanced        9.864  0.357  11.427
bisConversionControl           7.633  0.289   9.685
sesameQC_rankStats             6.777  0.885   8.371
prepSesame                     7.136  0.411   8.190
scrubSoft                      5.345  1.246   7.203
noMasked                       6.042  0.317   7.066
updateSigDF                    5.795  0.380   6.686
sdf_write_table                5.712  0.347   6.714
print.DMLSummary               4.830  1.055   6.435
parseGEOsignalMU               5.208  0.530   6.450
KYCG_plotWaterfall             5.366  0.304   6.178
summaryExtractTest             4.610  0.956   6.075
totalIntensities               5.207  0.328   6.205
checkLevels                    5.069  0.462   6.658
mapToMammal40                  4.920  0.429   5.915
meanIntensity                  4.737  0.587   6.015
KYCG_getDBs                    4.956  0.358   5.810
sesame-package                 4.752  0.555   5.763
dyeBiasCorr                    4.943  0.320   6.075
detectionPnegEcdf              5.040  0.190   6.521
qualityMask                    4.072  0.495   5.017
* 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 
 38.078   3.000  47.971