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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            65.705  4.494  72.889
imputeBetasByGenomicNeighbors 59.379  1.621  63.937
inferSex                      37.512  1.357  40.634
sesameQC_calcStats            34.832  2.790  39.457
KYCG_plotMeta                 32.814  1.125  36.139
sesameQC_plotHeatSNPs         29.388  1.809  32.738
KYCG_plotEnrichAll            29.590  1.580  32.840
compareMouseStrainReference   30.506  0.637  32.851
compareReference              28.405  1.155  31.226
imputeBetas                   26.350  1.679  29.742
KYCG_annoProbes               23.282  1.043  26.068
diffRefSet                    23.328  0.927  25.403
ELBAR                         21.457  2.711  26.182
matchDesign                   22.205  1.054  24.235
inferSpecies                  19.856  0.956  21.794
sesameQC_plotBar              19.423  0.595  20.878
KYCG_plotMetaEnrichment       18.495  0.640  20.043
getRefSet                     18.335  0.737  20.211
DML                           17.106  1.647  19.660
testEnrichmentSEA             15.973  1.649  19.709
KYCG_buildGeneDBs             16.059  0.628  17.618
sesameQC_plotBetaByDesign     15.522  0.986  17.417
sdf_read_table                15.667  0.645  17.112
visualizeGene                 15.514  0.693  17.184
DMR                           15.101  0.368  16.175
deidentify                    14.168  0.452  15.355
inferStrain                   13.223  0.848  14.848
inferTissue                   11.610  1.483  13.701
reIdentify                    12.440  0.533  13.514
dbStats                       10.611  0.840  16.475
getMask                       10.374  0.714  11.571
openSesame                     9.655  1.256  11.545
estimateLeukocyte             10.167  0.602  11.297
dyeBiasNL                     10.122  0.562  11.148
KYCG_plotSetEnrichment         9.819  0.539  10.816
createUCSCtrack                9.292  0.484  10.531
testEnrichment                 8.421  1.141   9.977
dyeBiasCorrMostBalanced        9.080  0.352   9.903
probeSuccessRate               8.533  0.750  10.094
bisConversionControl           7.510  0.304   8.251
noMasked                       6.056  0.679   7.016
visualizeProbes                6.422  0.262   7.054
prepSesame                     6.491  0.190   6.980
KYCG_plotWaterfall             6.214  0.364   6.877
scrubSoft                      5.234  1.282   6.875
sdf_write_table                5.726  0.341   6.501
updateSigDF                    5.583  0.448   6.400
sesameQC_rankStats             5.444  0.553   6.230
print.DMLSummary               4.593  1.255   6.260
parseGEOsignalMU               4.943  0.741   5.938
summaryExtractTest             4.297  1.147   6.035
totalIntensities               4.738  0.385   5.676
mapToMammal40                  4.579  0.486   5.236
detectionPnegEcdf              4.779  0.193   5.338
KYCG_getDBs                    4.556  0.359   5.214
* 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 
 37.093   3.229  44.204