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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_1.24.0.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            65.852  4.080  70.989
imputeBetasByGenomicNeighbors 57.293  1.548  59.667
inferSex                      37.527  1.264  39.336
sesameQC_calcStats            34.926  2.123  37.795
KYCG_plotMeta                 32.835  1.147  34.824
compareMouseStrainReference   31.485  0.669  49.348
KYCG_plotEnrichAll            28.810  1.626  31.249
sesameQC_plotHeatSNPs         28.513  1.309  30.424
compareReference              28.201  0.923  29.890
imputeBetas                   26.508  1.860  28.970
ELBAR                         22.851  3.388  26.591
diffRefSet                    23.788  0.841  25.158
KYCG_annoProbes               23.383  1.134  25.751
matchDesign                   21.301  1.020  22.625
inferSpecies                  20.255  1.000  21.450
sesameQC_plotBar              19.379  0.522  20.126
KYCG_plotMetaEnrichment       18.425  0.803  19.465
getRefSet                     18.259  0.603  19.229
sesameQC_plotBetaByDesign     17.269  1.430  18.948
DML                           16.918  1.655  19.255
visualizeGene                 17.134  0.767  18.044
testEnrichmentSEA             15.838  1.366  17.745
KYCG_buildGeneDBs             16.091  0.644  17.091
sdf_read_table                15.163  0.676  16.237
DMR                           15.062  0.373  15.616
deidentify                    14.152  0.441  14.805
inferStrain                   12.536  0.758  13.488
reIdentify                    11.870  0.321  12.580
inferTissue                   10.279  1.362  11.885
dbStats                       10.787  0.777  11.670
dyeBiasNL                     10.303  0.605  11.028
estimateLeukocyte             10.262  0.641  11.029
getMask                       10.189  0.658  10.969
KYCG_plotSetEnrichment         9.630  0.647  10.610
openSesame                     9.182  0.955  10.297
createUCSCtrack                9.424  0.506  10.313
dyeBiasCorrMostBalanced        9.195  0.415  10.224
testEnrichment                 8.367  1.031   9.580
probeSuccessRate               8.431  0.536   9.063
bisConversionControl           7.253  0.293   8.936
noMasked                       6.120  0.822   7.069
parseGEOsignalMU               5.421  1.201   3.746
scrubSoft                      5.240  1.243   6.674
prepSesame                     6.044  0.251   6.397
sesameQC_rankStats             5.631  0.323   6.475
updateSigDF                    5.470  0.468   6.033
print.DMLSummary               4.574  1.188   5.924
sdf_write_table                5.237  0.298   5.685
summaryExtractTest             4.093  1.130   5.419
detectionPnegEcdf              4.906  0.188   5.136
KYCG_getDBs                    4.614  0.405   5.078
totalIntensities               4.637  0.352   5.081
checkLevels                    4.517  0.459   5.928
KYCG_plotWaterfall             4.666  0.223   5.319
* 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 
 34.974   2.847  38.632