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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: 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 12.7.4
* 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            189.158  8.133 237.737
imputeBetasByGenomicNeighbors  62.576  1.709  74.361
inferSex                       38.817  1.270  44.888
sesameQC_calcStats             36.699  2.169  44.536
KYCG_plotMeta                  36.411  1.215  45.802
sesameQC_plotHeatSNPs          32.388  1.781  37.495
imputeBetas                    31.894  1.794  39.445
compareMouseStrainReference    32.650  0.998  39.369
KYCG_plotEnrichAll             31.979  1.430  38.270
compareReference               29.725  0.870  35.646
KYCG_annoProbes                25.347  1.353  31.231
ELBAR                          23.389  2.710  29.637
diffRefSet                     24.720  0.903  30.000
matchDesign                    22.910  1.156  27.576
inferSpecies                   21.028  1.090  25.154
sesameQC_plotBar               20.664  0.825  24.654
getRefSet                      20.783  0.696  25.144
KYCG_plotMetaEnrichment        20.256  0.722  23.340
DML                            17.791  2.054  25.169
testEnrichmentSEA              17.155  0.964  21.447
visualizeGene                  17.395  0.683  21.168
KYCG_buildGeneDBs              17.396  0.653  21.941
DMR                            17.002  0.524  20.858
sdf_read_table                 16.545  0.766  19.756
sesameQC_plotBetaByDesign      15.903  1.371  19.062
deidentify                     14.885  0.506  17.929
inferStrain                    14.338  1.008  17.492
inferTissue                    12.698  1.413  15.690
reIdentify                     12.994  0.348  15.162
estimateLeukocyte              12.317  0.628  15.032
getMask                        12.098  0.780  15.540
dbStats                        10.704  0.899  13.716
KYCG_plotSetEnrichment         10.845  0.565  13.324
openSesame                      9.959  0.745  12.200
createUCSCtrack                10.144  0.479  12.420
testEnrichment                  9.424  1.006  11.632
probeSuccessRate                9.581  0.839  11.917
dyeBiasCorrMostBalanced         9.922  0.394  12.142
dyeBiasNL                       8.565  0.543  10.787
bisConversionControl            7.809  0.304   9.210
prepSesame                      7.493  0.469   9.019
visualizeProbes                 6.872  0.202   8.165
scrubSoft                       5.471  1.301   7.444
sesameQC_rankStats              5.960  0.537   7.344
updateSigDF                     6.075  0.418   7.715
noMasked                        6.121  0.329   7.605
sdf_write_table                 5.833  0.352   6.964
KYCG_plotWaterfall              5.722  0.251   6.790
parseGEOsignalMU                5.334  0.617   6.873
print.DMLSummary                4.731  1.065   6.785
mapToMammal40                   5.275  0.501   6.791
summaryExtractTest              4.681  0.983   6.451
meanIntensity                   4.830  0.613   6.562
KYCG_getDBs                     5.014  0.375   6.203
totalIntensities                4.982  0.317   6.234
detectionPnegEcdf               5.056  0.232   6.431
dyeBiasCorr                     4.863  0.312   6.283
checkLevels                     4.652  0.353   6.080
KYCG_plotPointRange             4.716  0.243   5.666
sesame-package                  4.353  0.540   5.746
qualityMask                     4.244  0.574   5.633
dyeBiasL                        4.016  0.193   5.135
* 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 5 ]
> 
> proc.time()
   user  system elapsed 
 37.811   3.019  48.154