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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 (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* 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 45.593  1.397  63.673
inferSex                      30.157  0.998  42.884
sesameQC_calcStats            24.912  1.794  37.474
imputeBetas                   23.123  1.569  34.149
sesameQC_plotHeatSNPs         21.985  1.677  32.384
sesameQC_plotBar              21.035  0.645  29.649
inferSpecies                  20.666  0.897  29.229
ELBAR                         17.222  2.726  27.818
diffRefSet                    19.072  0.630  27.472
getRefSet                     18.539  0.542  26.086
matchDesign                   13.738  0.802  20.230
sesameQC_plotBetaByDesign     12.514  1.179  18.650
compareReference              12.309  0.456  18.650
visualizeGene                 11.985  0.658  17.596
compareMouseStrainReference   11.834  0.475  18.432
inferStrain                   11.441  0.529  16.995
sdf_read_table                11.421  0.485  16.676
DMR                           10.942  0.288  15.771
dyeBiasCorrMostBalanced       10.538  0.335  14.733
estimateLeukocyte              9.043  0.465  13.445
inferTissue                    8.241  0.944  12.619
getMask                        8.140  0.477  12.166
createUCSCtrack                8.160  0.393  12.162
probeSuccessRate               7.443  0.670  11.620
DML                            7.680  0.291  10.889
bisConversionControl           7.413  0.235  10.446
openSesame                     6.269  0.767  10.114
deIdentify                     6.434  0.358   9.452
dyeBiasNL                      6.036  0.380   8.553
reIdentify                     5.332  0.303   7.729
checkLevels                    5.416  0.210   7.540
prepSesame                     4.476  0.596   6.605
scrubSoft                      4.157  0.865   6.760
noMasked                       4.459  0.235   6.564
updateSigDF                    4.158  0.501   6.561
summaryExtractTest             4.050  0.566   6.367
parseGEOsignalMU               4.162  0.285   6.181
print.DMLSummary               3.871  0.525   5.880
sesameQC_rankStats             3.780  0.324   5.786
mapToMammal40                  3.367  0.391   5.254
predictAge                     3.533  0.150   5.393
dyeBiasCorr                    3.292  0.236   5.369
* 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-arm64/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 (2025-11-04 r88984) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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
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 
 24.671   0.939  35.632