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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            67.294  4.529  73.748
imputeBetasByGenomicNeighbors 57.773  1.552  60.682
inferSex                      36.777  1.369  38.663
sesameQC_calcStats            34.011  2.707  37.383
KYCG_plotMeta                 32.964  1.270  35.521
sesameQC_plotHeatSNPs         29.943  2.059  32.438
compareMouseStrainReference   30.596  0.666  32.328
KYCG_plotEnrichAll            29.439  1.623  31.741
compareReference              28.194  1.027  30.431
imputeBetas                   25.729  1.875  28.156
ELBAR                         21.334  3.493  25.298
diffRefSet                    23.315  1.013  24.821
KYCG_annoProbes               23.030  1.174  24.940
matchDesign                   21.904  0.966  23.159
inferSpecies                  20.952  0.945  22.082
sesameQC_plotBar              19.077  0.597  20.088
getRefSet                     18.398  0.756  19.359
KYCG_plotMetaEnrichment       18.352  0.785  19.501
DML                           17.151  1.667  20.048
sesameQC_plotBetaByDesign     16.089  1.088  17.403
testEnrichmentSEA             15.673  1.270  17.142
KYCG_buildGeneDBs             16.166  0.638  17.487
sdf_read_table                15.622  0.657  16.817
visualizeGene                 15.566  0.667  16.345
DMR                           15.185  0.389  16.198
deidentify                    14.263  0.499  15.176
inferStrain                   12.794  0.777  13.841
reIdentify                    12.668  0.499  13.303
inferTissue                   11.219  1.419  12.813
dbStats                       10.638  0.919  11.715
estimateLeukocyte             10.343  0.633  11.081
getMask                       10.134  0.789  11.168
dyeBiasNL                      9.995  0.588  10.835
openSesame                     9.414  0.992  10.596
KYCG_plotSetEnrichment         9.701  0.643  10.532
createUCSCtrack                9.511  0.481  10.239
testEnrichment                 8.573  1.107   9.836
dyeBiasCorrMostBalanced        9.144  0.373   9.648
probeSuccessRate               8.430  0.655   9.289
bisConversionControl           7.433  0.330   7.870
visualizeProbes                6.700  0.104   6.820
noMasked                       6.011  0.615   6.730
scrubSoft                      5.167  1.410   6.663
KYCG_plotWaterfall             6.097  0.402   6.579
prepSesame                     6.236  0.238   6.542
sdf_write_table                5.826  0.326   6.521
updateSigDF                    5.666  0.439   6.176
sesameQC_rankStats             5.453  0.440   5.963
parseGEOsignalMU               5.103  0.676   5.856
print.DMLSummary               4.422  0.991   5.457
summaryExtractTest             4.213  0.969   5.421
totalIntensities               4.753  0.332   5.178
KYCG_getDBs                    4.603  0.418   5.072
* 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 
 35.948   2.782  39.044