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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_1.18.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.18.4’
* 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘BiocManager’
* 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          173.361  6.526 236.118
sesameQC_calcStats           37.981  1.761  48.613
KYCG_plotMeta                33.412  1.046  44.335
sesameQC_plotHeatSNPs        32.513  1.578  43.312
KYCG_plotEnrichAll           30.465  1.315  42.394
compareMouseStrainReference  29.723  0.540  38.934
compareReference             26.657  0.814  35.554
inferSpecies                 25.258  1.095  33.831
ELBAR                        22.487  2.761  33.658
matchDesign                  23.871  1.162  33.146
diffRefSet                   22.882  0.716  30.375
KYCG_annoProbes              21.978  0.996  30.883
sesameQC_plotBar             19.909  0.484  26.432
KYCG_plotMetaEnrichment      18.611  0.644  25.561
testEnrichmentSEA            18.267  0.950  24.342
getRefSet                    18.498  0.670  25.096
sesameQC_plotBetaByDesign    17.744  1.048  23.893
inferTissue                  16.302  1.479  23.587
DML                          15.681  1.656  23.544
KYCG_buildGeneDBs            16.132  0.588  22.851
sdf_read_table               15.404  0.611  20.553
visualizeGene                15.469  0.543  20.231
DMR                          15.552  0.427  21.475
getSexInfo                   14.561  0.606  19.538
deidentify                   13.706  0.460  18.901
inferStrain                  12.707  0.875  17.590
reIdentify                   12.107  0.344  17.342
estimateLeukocyte             9.939  0.546  14.246
dbStats                       9.333  0.706  13.379
KYCG_plotSetEnrichment        9.390  0.524  12.912
dyeBiasNL                     9.201  0.554  12.324
dyeBiasCorrMostBalanced       9.290  0.320  12.605
openSesame                    8.730  0.774  12.438
createUCSCtrack               9.035  0.335  12.903
probeSuccessRate              8.490  0.672  12.209
testEnrichment                8.068  0.558  12.218
inferSex                      8.027  0.470  10.982
getMask                       7.583  0.518  10.991
bisConversionControl          7.487  0.295  10.154
visualizeProbes               7.512  0.238   9.618
prepSesame                    6.246  0.427   8.585
sdf_write_table               5.733  0.324   7.543
scrubSoft                     5.365  0.644   7.568
sesameQC_rankStats            5.678  0.303   8.139
inferSexKaryotypes            5.361  0.260   7.238
formatVCF                     5.237  0.374   7.368
KYCG_plotWaterfall            5.002  0.206   7.060
totalIntensities              4.770  0.386   6.514
KYCG_getDBs                   4.774  0.340   6.883
mapToMammal40                 4.700  0.384   7.100
print.DMLSummary              3.949  1.027   6.437
updateSigDF                   4.625  0.302   6.400
detectionPnegEcdf             4.714  0.159   6.704
parseGEOsignalMU              4.651  0.197   6.078
checkLevels                   4.407  0.428   6.325
dyeBiasCorr                   4.326  0.264   6.146
meanIntensity                 4.183  0.314   5.873
summaryExtractTest            3.728  0.692   6.136
qualityMask                   3.741  0.469   6.334
scrub                         3.844  0.297   5.488
sesameQC_getStats             3.933  0.188   5.083
sesame-package                3.643  0.458   5.063
KYCG_plotPointRange           3.821  0.212   5.218
inferEthnicity                3.675  0.245   5.244
noMasked                      3.271  0.467   5.095
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck/00check.log’
for details.

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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/4.3-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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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, sort, 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 
 34.235   3.281  46.803