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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 4.4.3 (2025-02-28)
* 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            66.512  4.404  72.164
imputeBetasByGenomicNeighbors 58.896  1.698  61.592
inferSex                      37.770  1.407  39.536
sesameQC_calcStats            35.343  2.151  39.129
KYCG_plotMeta                 32.005  1.210  33.613
sesameQC_plotHeatSNPs         29.454  1.486  31.511
KYCG_plotEnrichAll            28.678  1.651  31.070
compareMouseStrainReference   29.395  0.600  32.264
imputeBetas                   27.331  1.972  29.936
compareReference              27.556  0.888  29.471
ELBAR                         23.025  3.274  27.157
diffRefSet                    23.477  0.884  24.483
KYCG_annoProbes               23.204  1.144  24.652
matchDesign                   21.111  0.998  22.241
inferSpecies                  19.318  1.039  20.618
sesameQC_plotBar              19.502  0.511  20.890
getRefSet                     18.698  0.618  19.467
KYCG_plotMetaEnrichment       18.009  0.711  18.994
sesameQC_plotBetaByDesign     17.307  1.403  18.859
DML                           16.917  1.674  18.778
visualizeGene                 17.420  0.883  18.707
testEnrichmentSEA             16.189  1.273  17.601
KYCG_buildGeneDBs             15.929  0.651  16.760
sdf_read_table                15.079  0.744  18.222
DMR                           15.163  0.390  16.314
deidentify                    14.363  0.472  15.184
inferStrain                   12.333  0.732  13.292
inferTissue                   10.631  1.445  12.219
reIdentify                    11.714  0.250  12.127
dbStats                       11.027  0.846  11.957
dyeBiasNL                     10.847  0.568  11.492
estimateLeukocyte             10.621  0.692  11.607
getMask                       10.418  0.729  11.238
openSesame                     9.539  1.024  10.844
KYCG_plotSetEnrichment         9.377  0.625  10.056
testEnrichment                 8.707  1.156  10.025
createUCSCtrack                9.369  0.445  10.109
dyeBiasCorrMostBalanced        9.202  0.337   9.574
probeSuccessRate               8.531  0.581   9.205
bisConversionControl           7.279  0.333  21.358
parseGEOsignalMU               5.446  1.270   6.791
noMasked                       5.943  0.636   6.677
prepSesame                     6.005  0.337   6.451
scrubSoft                      5.117  1.219   6.417
updateSigDF                    5.745  0.458   6.235
sesameQC_rankStats             5.705  0.319   6.091
print.DMLSummary               4.611  1.335   6.072
summaryExtractTest             4.279  1.157   5.524
sdf_write_table                5.111  0.324   5.991
detectionPnegEcdf              4.998  0.211   5.251
checkLevels                    4.619  0.466   5.138
totalIntensities               4.731  0.338   5.112
KYCG_plotWaterfall             4.812  0.249   5.184
KYCG_getDBs                    4.600  0.367   5.033
mapToMammal40                  4.489  0.448   5.052
dyeBiasCorr                    4.592  0.337   5.005
* 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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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 
 36.869   2.820  40.691