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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_1.22.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 (2024-04-24)
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.22.1’
* 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
testEnrichmentGene            166.472  6.396 268.419
imputeBetasByGenomicNeighbors  50.170  1.322  72.243
KYCG_plotMeta                  32.890  1.044  48.812
inferSex                       31.208  0.937  47.674
sesameQC_plotHeatSNPs          27.921  1.007  44.381
KYCG_plotEnrichAll             27.328  1.405  41.329
imputeBetas                    26.227  1.388  39.423
ELBAR                          23.503  2.380  34.361
sesameQC_calcStats             24.451  1.314  37.513
inferSpecies                   21.666  0.865  34.615
KYCG_annoProbes                19.818  0.905  29.815
diffRefSet                     18.855  0.691  27.976
sesameQC_plotBar               18.663  0.459  28.286
KYCG_plotMetaEnrichment        16.958  0.703  26.737
getRefSet                      16.919  0.533  23.856
testEnrichmentSEA              15.657  0.961  26.231
KYCG_buildGeneDBs              15.882  0.530  23.662
sesameQC_plotBetaByDesign      13.997  0.994  22.671
matchDesign                    13.943  0.717  22.418
compareMouseStrainReference    13.359  0.555  20.053
inferStrain                    13.181  0.610  21.313
visualizeGene                  12.607  0.521  20.144
compareReference               12.281  0.501  18.233
inferTissue                    10.751  1.204  17.808
DMR                            11.459  0.338  18.114
estimateLeukocyte              11.244  0.513  17.349
sdf_read_table                 10.348  0.821  17.296
dbStats                        10.177  0.605  16.039
DML                             9.601  1.007  15.582
getMask                         9.275  0.631  14.693
testEnrichment                  8.159  0.968  14.449
createUCSCtrack                 8.433  0.516  12.373
dyeBiasCorrMostBalanced         8.275  0.349  12.632
KYCG_plotSetEnrichment          7.814  0.443  12.246
openSesame                      7.566  0.664  13.332
probeSuccessRate                7.154  0.780  12.531
bisConversionControl            6.563  0.281  10.128
dyeBiasNL                       6.507  0.311   9.663
visualizeRegion                 6.443  0.088   9.561
deidentify                      5.853  0.479   9.419
prepSesame                      5.327  0.368   9.633
print.DMLSummary                4.601  0.646   9.165
summaryExtractTest              4.647  0.590   8.782
mapToMammal40                   4.388  0.675   8.316
reIdentify                      4.869  0.193   7.936
totalIntensities                4.563  0.297   7.890
sesameQC_rankStats              4.323  0.269   7.356
noMasked                        4.259  0.280   7.407
dyeBiasL                        4.274  0.140   6.417
checkLevels                     4.140  0.264   6.311
aggregateTestEnrichments        4.013  0.101   5.814
KYCG_plotWaterfall              3.865  0.235   6.067
parseGEOsignalMU                3.677  0.269   6.304
updateSigDF                     3.611  0.307   6.286
KYCG_getDBs                     3.609  0.297   5.795
KYCG_plotPointRange             3.638  0.217   5.706
meanIntensity                   3.362  0.405   6.015
qualityMask                     3.332  0.370   5.327
scrubSoft                       3.184  0.515   5.104
visualizeSegments               3.163  0.520   6.182
dyeBiasCorr                     3.282  0.272   5.130
predictAge                      3.295  0.171   5.363
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
 28.267   1.814  46.396