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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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-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 Monterey 12.7.1
* 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          175.243  7.356 196.168
sesameQC_calcStats           35.500  1.511  38.794
KYCG_plotMeta                33.043  1.225  36.879
KYCG_plotEnrichAll           29.863  1.509  33.709
sesameQC_plotHeatSNPs        28.876  1.964  32.417
compareMouseStrainReference  29.546  0.581  32.098
compareReference             26.005  0.778  28.387
ELBAR                        21.755  3.220  25.825
matchDesign                  23.773  0.953  25.910
inferSpecies                 23.782  0.919  26.373
KYCG_annoProbes              22.294  0.975  25.114
diffRefSet                   21.319  0.683  23.155
convertTo                    20.780  0.775  22.628
sesameQC_plotBar             19.703  0.476  21.677
testEnrichmentSEA            18.667  1.071  21.108
sesameQC_plotBetaByDesign    17.587  1.490  20.213
getRefSet                    18.382  0.621  23.090
DML                          16.521  1.719  19.227
KYCG_plotMetaEnrichment      17.250  0.799  20.092
inferTissue                  16.141  1.468  18.750
KYCG_buildGeneDBs            15.867  0.598  17.649
visualizeGene                15.817  0.583  18.107
sdf_read_table               14.756  0.845  21.661
DMR                          14.262  0.429  15.082
getSexInfo                   13.790  0.599  15.183
inferStrain                  13.229  0.881  14.722
deidentify                   13.479  0.481  14.680
dbStats                      11.699  0.940  13.543
reIdentify                   12.002  0.406  13.158
createUCSCtrack              11.338  0.411  12.562
dyeBiasNL                    10.291  0.664  11.593
estimateLeukocyte            10.075  0.600  11.411
KYCG_plotSetEnrichment        9.479  0.597  10.840
probeSuccessRate              9.103  0.611  10.721
openSesame                    9.103  0.571  10.391
dyeBiasCorrMostBalanced       9.222  0.342  10.433
testEnrichment                8.412  0.905   9.695
getMask                       8.133  0.533   9.471
inferSex                      7.775  0.477   8.690
bisConversionControl          7.496  0.345   8.324
visualizeProbes               7.388  0.211   8.310
KYCG_plotWaterfall            6.592  0.262   7.220
scrubSoft                     5.544  0.839   6.609
print.DMLSummary              5.242  1.137   7.061
prepSesame                    6.154  0.171   6.769
sesameQC_rankStats            5.327  0.538   6.232
KYCG_plotPointRange           5.291  0.259   6.580
sdf_write_table               5.164  0.383   8.659
parseGEOsignalMU              5.082  0.461   6.008
inferSexKaryotypes            5.016  0.289   5.611
totalIntensities              4.901  0.396   5.943
updateSigDF                   4.914  0.355   5.984
detectionPnegEcdf             4.969  0.179   5.444
mapToMammal40                 4.752  0.385   5.470
checkLevels                   4.449  0.535   5.415
qualityMask                   4.608  0.339   5.447
KYCG_getDBs                   4.544  0.374   5.213
dyeBiasCorr                   4.496  0.330   5.383
summaryExtractTest            4.065  0.743   5.301
meanIntensity                 4.372  0.284   5.529
sesame-package                4.060  0.537   5.114
* 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-x86_64/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: x86_64-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 
 35.098   2.797  39.710