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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: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.23.6’
* 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            67.016  3.272  75.268
imputeBetasByGenomicNeighbors 46.111  1.274  48.797
inferSex                      28.008  0.905  29.818
sesameQC_calcStats            25.502  1.983  28.114
KYCG_plotMeta                 26.176  1.044  28.520
KYCG_plotEnrichAll            25.343  0.991  29.231
imputeBetas                   23.927  1.442  29.980
sesameQC_plotHeatSNPs         21.918  1.478  23.866
sesameQC_plotBar              19.858  0.457  21.175
ELBAR                         16.433  2.828  19.843
inferSpecies                  18.427  0.719  20.493
KYCG_annoProbes               17.485  0.724  19.739
diffRefSet                    17.511  0.631  18.987
getRefSet                     16.731  0.428  20.886
KYCG_plotMetaEnrichment       15.647  0.559  17.773
KYCG_buildGeneDBs             14.925  0.488  16.741
testEnrichmentSEA             14.064  1.020  16.251
matchDesign                   14.245  0.743  15.441
visualizeGene                 13.913  0.448  15.531
sesameQC_plotBetaByDesign     12.260  1.497  13.813
compareMouseStrainReference   12.604  0.605  14.117
compareReference              11.409  0.379  12.815
inferStrain                   11.251  0.495  12.612
sdf_read_table                11.027  0.669  12.533
DMR                            9.921  0.235  10.948
dyeBiasCorrMostBalanced        9.781  0.271  10.858
estimateLeukocyte              9.481  0.418  11.417
DML                            8.581  0.840  10.588
getMask                        8.780  0.517  12.520
inferTissue                    8.032  1.075  10.056
createUCSCtrack                8.340  0.398   9.529
dbStats                        7.729  0.491   9.035
probeSuccessRate               7.480  0.634   9.651
testEnrichment                 7.102  0.654   8.877
bisConversionControl           7.508  0.213   8.509
openSesame                     6.878  0.608   8.332
KYCG_plotSetEnrichment         6.376  0.466   7.611
deidentify                     6.049  0.376   7.241
dyeBiasNL                      5.150  0.399   5.943
prepSesame                     4.715  0.332   5.449
reIdentify                     4.637  0.163   5.229
mapToMammal40                  4.138  0.575   5.544
noMasked                       4.461  0.216   5.486
summaryExtractTest             3.954  0.525   5.249
totalIntensities               4.166  0.255   5.187
updateSigDF                    4.108  0.307   5.180
* 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-arm64/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: aarch64-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 
 25.518   1.393  27.885