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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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-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 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 ‘1.24.0’
* 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 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            66.856  4.703  74.106
imputeBetasByGenomicNeighbors 59.545  1.671  63.788
inferSex                      38.361  1.399  40.966
sesameQC_calcStats            34.695  3.128  38.423
KYCG_plotMeta                 32.664  1.343  38.471
sesameQC_plotHeatSNPs         30.761  2.668  33.995
KYCG_plotEnrichAll            29.605  1.667  32.516
compareMouseStrainReference   30.470  0.670  32.058
compareReference              28.488  1.219  33.142
imputeBetas                   26.392  1.898  29.272
KYCG_annoProbes               23.328  1.224  26.047
diffRefSet                    23.494  1.005  25.550
ELBAR                         21.291  3.166  25.318
matchDesign                   22.217  1.104  24.011
inferSpecies                  20.764  1.071  22.570
sesameQC_plotBar              19.276  0.656  20.289
KYCG_plotMetaEnrichment       18.621  0.741  20.602
getRefSet                     18.490  0.767  19.840
DML                           17.289  1.728  20.674
testEnrichmentSEA             15.786  1.563  17.801
sesameQC_plotBetaByDesign     16.079  1.237  17.765
KYCG_buildGeneDBs             16.244  0.692  18.010
sdf_read_table                15.681  0.702  16.968
visualizeGene                 15.523  0.723  16.587
DMR                           15.215  0.403  16.474
deidentify                    14.455  0.533  15.449
inferStrain                   13.949  0.881  15.219
inferTissue                   11.879  1.671  14.344
reIdentify                    12.809  0.660  13.837
dbStats                       10.818  0.892  12.493
estimateLeukocyte             10.556  0.659  11.809
dyeBiasNL                     10.480  0.567  11.589
getMask                       10.333  0.698  11.373
openSesame                     9.675  1.345  11.655
KYCG_plotSetEnrichment         9.830  0.623  11.024
createUCSCtrack                9.685  0.522  11.209
dyeBiasCorrMostBalanced        9.440  0.418  10.311
testEnrichment                 8.744  1.066  10.067
probeSuccessRate               8.477  0.803   9.484
bisConversionControl           7.380  0.337   8.103
visualizeProbes                6.500  0.304   7.064
prepSesame                     6.504  0.253   6.970
noMasked                       6.054  0.696   6.821
scrubSoft                      5.271  1.433   6.804
KYCG_plotWaterfall             6.067  0.351   6.599
print.DMLSummary               4.809  1.402   6.673
sdf_write_table                5.797  0.361   6.411
sesameQC_rankStats             5.484  0.532   6.109
updateSigDF                    5.340  0.525   5.921
parseGEOsignalMU               4.940  0.825   5.906
summaryExtractTest             4.483  1.179   5.794
totalIntensities               4.733  0.361   5.294
KYCG_getDBs                    4.652  0.381   5.177
detectionPnegEcdf              4.812  0.200   5.165
dyeBiasCorr                    4.580  0.321   5.138
mapToMammal40                  4.335  0.444   5.160
* 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-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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

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, saveRDS, 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 
 36.082   3.336  41.949