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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-mac-arm64/meat/sesame.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 12.6.7
* 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          145.560  4.786 285.599
KYCG_plotMeta                25.007  0.763  47.042
sesameQC_plotHeatSNPs        24.276  0.800  45.057
sesameQC_calcStats           23.608  1.028  45.229
KYCG_plotEnrichAll           23.581  0.979  47.042
inferSpecies                 18.344  0.725  34.708
matchDesign                  17.607  0.590  33.236
testEnrichmentSEA            15.606  1.573  32.915
sesameQC_plotBar             15.835  1.018  30.609
ELBAR                        15.408  1.062  27.642
KYCG_annoProbes              15.526  0.580  29.860
diffRefSet                   15.245  0.453  27.745
compareMouseStrainReference  14.583  0.493  27.299
getRefSet                    13.987  0.417  26.517
KYCG_plotMetaEnrichment      12.766  0.439  23.861
KYCG_buildGeneDBs            12.012  0.475  22.956
inferTissue                  11.753  0.642  23.422
visualizeGene                11.829  0.561  23.867
compareReference             11.837  0.448  21.719
sesameQC_plotBetaByDesign    11.286  0.767  20.736
getSexInfo                   11.311  0.467  24.610
sdf_read_table               10.565  0.682  21.074
DMR                           9.950  0.277  18.690
DML                           9.118  0.992  24.864
inferStrain                   9.099  0.500  18.505
createUCSCtrack               8.389  0.361  16.303
probeSuccessRate              8.189  0.478  16.687
testEnrichment                7.863  0.556  16.537
dbStats                       7.656  0.406  15.240
estimateLeukocyte             7.591  0.336  14.551
dyeBiasCorrMostBalanced       7.179  0.254  13.898
getMask                       7.043  0.371  15.256
dyeBiasNL                     7.057  0.188  13.190
openSesame                    6.680  0.518  13.931
deidentify                    6.770  0.349  13.758
KYCG_plotSetEnrichment        6.553  0.286  12.732
updateSigDF                   5.943  0.500  12.493
mapToMammal40                 5.656  0.417  11.757
reIdentify                    5.753  0.172  10.898
visualizeProbes               5.550  0.263  11.019
bisConversionControl          5.593  0.205  11.034
inferSex                      5.311  0.213  10.423
inferSexKaryotypes            5.197  0.131   8.888
print.DMLSummary              4.143  0.617   9.265
sesameQC_rankStats            4.389  0.236   8.959
formatVCF                     4.155  0.296   8.847
KYCG_plotPointRange           4.288  0.158   7.472
KYCG_getDBs                   4.166  0.255   8.798
sesame-package                3.791  0.539   8.038
prepSesame                    4.006  0.267   8.305
totalIntensities              3.728  0.427   8.468
qualityMask                   3.630  0.235   7.309
parseGEOsignalMU              3.580  0.219   7.535
scrubSoft                     3.406  0.392   6.533
predictAge                    3.436  0.199   7.007
sdf_write_table               3.328  0.298   6.945
checkLevels                   3.383  0.186   6.761
meanIntensity                 3.294  0.234  13.573
summaryExtractTest            3.174  0.310   7.270
dyeBiasCorr                   3.253  0.196   6.688
KYCG_plotWaterfall            3.236  0.153   6.407
detectionPnegEcdf             3.140  0.134   6.358
inferEthnicity                2.959  0.158   5.594
listAvailableMasks            2.547  0.213   5.159
noMasked                      2.443  0.245   5.293
sesameQC_plotIntensVsBetas    2.529  0.098   5.279
controls                      2.415  0.174   5.499
* 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-mac-arm64/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-arm64/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: aarch64-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 
 21.933   2.317  42.376