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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_1.21.12.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.21.12’
* 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 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          176.358  7.695 216.738
inferSex                     54.830  2.057  66.562
sesameQC_calcStats           34.887  1.631  42.412
KYCG_plotMeta                32.151  1.307  39.819
KYCG_plotEnrichAll           29.770  1.572  38.615
compareMouseStrainReference  30.048  0.899  37.495
sesameQC_plotHeatSNPs        29.049  1.293  35.065
compareReference             27.188  1.150  32.918
matchDesign                  23.919  1.124  29.379
ELBAR                        21.927  2.938  30.698
KYCG_annoProbes              23.091  1.127  29.319
diffRefSet                   23.110  0.947  29.573
inferSpecies                 21.250  1.225  26.542
sesameQC_plotBar             19.736  0.513  23.745
KYCG_plotMetaEnrichment      18.828  0.926  23.666
DML                          16.966  2.662  31.976
getRefSet                    18.377  0.693  22.383
sesameQC_plotBetaByDesign    16.648  1.959  22.239
KYCG_buildGeneDBs            16.313  0.652  20.006
sdf_read_table               15.716  0.991  19.864
testEnrichmentSEA            15.562  0.933  20.388
visualizeGene                15.357  0.655  19.399
DMR                          14.964  0.449  19.397
deidentify                   14.047  0.496  18.034
inferStrain                  12.906  0.935  15.917
inferTissue                  11.157  1.495  14.709
estimateLeukocyte            11.477  0.650  14.209
reIdentify                   11.762  0.348  14.105
dbStats                       9.955  0.870  13.375
KYCG_plotSetEnrichment        9.601  0.627  12.079
openSesame                    9.249  0.920  12.050
createUCSCtrack               9.485  0.453  11.955
dyeBiasNL                     9.305  0.611  11.967
dyeBiasCorrMostBalanced       9.224  0.418  11.575
testEnrichment                8.614  0.846  11.266
probeSuccessRate              8.689  0.540  11.164
getMask                       7.997  0.549  10.160
bisConversionControl          7.180  0.338  12.890
prepSesame                    6.159  0.218   7.540
sesameQC_rankStats            5.770  0.356   7.153
scrubSoft                     5.168  0.818   6.972
print.DMLSummary              4.734  1.048   6.929
parseGEOsignalMU              5.107  0.571   6.746
summaryExtractTest            4.615  1.016   6.696
sdf_write_table               5.048  0.391   6.560
qualityMask                   4.792  0.642   6.592
updateSigDF                   4.968  0.370   6.485
KYCG_plotWaterfall            5.079  0.257   6.866
totalIntensities              4.958  0.340   6.318
mapToMammal40                 4.749  0.426   6.268
KYCG_getDBs                   4.731  0.409   6.623
detectionPnegEcdf             4.929  0.209   6.187
dyeBiasCorr                   4.532  0.341   6.102
meanIntensity                 4.488  0.324   6.162
checkLevels                   4.399  0.373   7.545
* 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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
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, 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 1 ]
> 
> proc.time()
   user  system elapsed 
 34.529   2.963  45.440