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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_1.28.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/sesame.Rcheck’
* using R version 4.5.2 Patched (2025-11-05 r88990)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.28.1’
* 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
imputeBetasByGenomicNeighbors 60.240  1.582  62.706
inferSex                      37.992  1.167  39.688
sesameQC_calcStats            33.835  1.821  36.218
compareMouseStrainReference   29.658  0.808  31.010
sesameQC_plotHeatSNPs         27.896  1.784  30.179
imputeBetas                   27.104  1.827  29.108
compareReference              27.331  0.857  28.313
diffRefSet                    24.442  0.837  27.811
ELBAR                         21.708  3.278  25.567
inferSpecies                  23.130  0.908  24.393
matchDesign                   21.594  0.842  22.993
getRefSet                     19.862  0.767  21.101
sesameQC_plotBar              19.739  0.557  20.428
sesameQC_plotBetaByDesign     15.838  1.213  17.187
DMR                           15.930  0.426  16.674
sdf_read_table                15.516  0.699  16.420
visualizeGene                 14.788  0.939  15.896
inferStrain                   14.829  0.761  15.674
deIdentify                    14.033  0.594  14.917
DML                           13.577  0.575  14.336
inferTissue                   11.947  1.649  13.672
reIdentify                    11.930  0.405  12.471
estimateLeukocyte             10.677  0.618  11.589
getMask                       10.202  0.775  11.105
openSesame                     9.171  1.481  10.776
dyeBiasCorrMostBalanced       10.099  0.454  11.072
createUCSCtrack                9.122  0.496   9.715
dyeBiasNL                      8.772  0.529   9.472
probeSuccessRate               8.419  0.802   9.251
bisConversionControl           6.918  0.333   7.314
prepSesame                     6.218  0.520   6.774
scrubSoft                      5.241  1.142   6.437
noMasked                       5.789  0.305   6.148
checkLevels                    5.517  0.351   5.930
updateSigDF                    5.067  0.748   5.858
sdf_write_table                5.298  0.327   5.662
sesameQC_rankStats             4.968  0.421   5.433
summaryExtractTest             4.302  1.078   5.559
print.DMLSummary               4.354  0.903   5.294
parseGEOsignalMU               4.690  0.303   5.142
dyeBiasCorr                    4.612  0.355   5.054
meanIntensity                  4.454  0.499   5.080
* 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/4.5-x86_64/Resources/library’
* installing *source* package ‘sesame’ ...
** this is package ‘sesame’ version ‘1.28.1’
** 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 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, 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 
 33.341   1.789  36.267