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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_1.22.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘1.22.2’
* 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            166.284  6.213 184.789
imputeBetasByGenomicNeighbors  45.271  1.723  53.389
inferSex                       30.618  1.114  33.961
sesameQC_calcStats             26.181  2.589  30.112
KYCG_plotMeta                  27.313  1.173  31.967
KYCG_plotEnrichAll             26.993  1.058  31.912
imputeBetas                    24.099  2.093  28.650
sesameQC_plotHeatSNPs          22.659  1.342  25.616
ELBAR                          16.908  3.579  21.368
sesameQC_plotBar               19.405  0.489  21.818
inferSpecies                   18.382  0.824  21.481
diffRefSet                     17.821  0.845  22.058
KYCG_annoProbes                17.864  0.754  20.769
getRefSet                      17.293  0.609  19.997
KYCG_plotMetaEnrichment        16.409  0.715  21.293
KYCG_buildGeneDBs              15.466  0.580  17.815
visualizeGene                  14.240  0.575  16.237
sesameQC_plotBetaByDesign      12.654  2.148  15.849
matchDesign                    13.971  0.799  15.563
testEnrichmentSEA              13.909  0.855  16.118
compareMouseStrainReference    13.388  0.612  16.519
compareReference               12.195  0.490  14.850
sdf_read_table                 11.367  0.721  13.058
inferStrain                    10.880  0.726  12.827
DMR                            10.580  0.290  11.922
estimateLeukocyte               9.936  0.494  12.708
dyeBiasCorrMostBalanced        10.077  0.351  12.460
DML                             9.123  0.932  11.218
getMask                         9.423  0.553  12.897
dbStats                         8.803  0.711  11.436
createUCSCtrack                 8.764  0.472  11.258
openSesame                      7.440  0.848   9.331
testEnrichment                  7.542  0.730   9.895
bisConversionControl            7.753  0.246   9.676
probeSuccessRate                7.366  0.628  10.320
inferTissue                     6.398  1.037   8.897
KYCG_plotSetEnrichment          6.407  0.587   8.786
deidentify                      5.862  0.370   7.578
dyeBiasNL                       5.210  0.641   6.953
mapToMammal40                   4.772  0.451   6.162
noMasked                        4.653  0.340   5.924
prepSesame                      4.586  0.322   5.657
reIdentify                      4.724  0.147   5.854
totalIntensities                4.435  0.269   5.553
parseGEOsignalMU                4.327  0.238   5.052
summaryExtractTest              3.987  0.538   5.828
print.DMLSummary                3.795  0.505   5.237
sesameQC_rankStats              3.809  0.362   5.104
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
 25.702   1.683  29.050