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### Running command:
###
###   /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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/sesame.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.20.0’
* 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 R 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 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          175.219  5.528 195.484
KYCG_plotEnrichAll           28.014  1.141  33.895
KYCG_plotMeta                25.915  1.285  30.406
sesameQC_calcStats           25.174  1.374  28.439
sesameQC_plotHeatSNPs        23.300  1.990  26.979
inferSpecies                 22.619  0.961  26.196
convertTo                    22.482  0.590  24.576
sesameQC_plotBar             21.381  0.686  24.238
matchDesign                  19.801  1.083  22.329
ELBAR                        15.999  3.359  20.070
testEnrichmentSEA            17.133  0.927  19.658
KYCG_annoProbes              17.022  0.608  19.269
diffRefSet                   16.795  0.691  19.402
getRefSet                    16.168  0.606  18.746
visualizeGene                15.280  0.489  17.284
KYCG_plotMetaEnrichment      14.284  0.628  16.928
KYCG_buildGeneDBs            14.019  0.429  15.394
getSexInfo                   13.664  0.784  16.235
inferTissue                  12.646  0.852  15.362
compareMouseStrainReference  12.314  0.476  14.292
compareReference             12.210  0.467  13.556
sesameQC_plotBetaByDesign    11.295  1.041  12.942
sdf_read_table               11.225  0.468  13.444
dyeBiasCorrMostBalanced      11.032  0.297  12.841
estimateLeukocyte            10.583  0.493  12.543
DMR                          10.109  0.267  11.676
inferStrain                   9.274  0.812  11.378
DML                           8.386  0.846  10.253
createUCSCtrack               8.868  0.291  10.501
dbStats                       8.280  0.593   9.975
probeSuccessRate              8.117  0.565  10.598
testEnrichment                7.941  0.704  10.112
bisConversionControl          8.027  0.283   9.803
getMask                       7.597  0.437  10.191
KYCG_plotSetEnrichment        6.572  0.573   8.283
dyeBiasNL                     6.382  0.714   8.172
deidentify                    6.319  0.493   7.862
visualizeProbes               6.433  0.152   7.093
openSesame                    6.131  0.450   7.923
inferSex                      5.741  0.466   7.306
prepSesame                    5.644  0.539   6.873
mapToMammal40                 5.573  0.422   7.057
reIdentify                    5.329  0.246   6.300
scrubSoft                     3.950  1.138   5.378
qualityMask                   4.625  0.414   6.073
parseGEOsignalMU              4.565  0.321   5.539
KYCG_plotPointRange           4.657  0.201   5.518
inferSexKaryotypes            4.575  0.271   5.486
summaryExtractTest            4.193  0.439   5.659
sesameQC_rankStats            4.038  0.516   5.545
totalIntensities              4.041  0.244   5.108
updateSigDF                   3.878  0.245   5.196
KYCG_getDBs                   3.853  0.234   5.140
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

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, sort, 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 1 ]
> 
> proc.time()
   user  system elapsed 
 25.984   1.506  28.791