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### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings sesame_1.19.10.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.19.10’
* 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 loading without being on the library search path ... OK
* checking 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          128.352  4.393 155.183
sesameQC_calcStats           31.012  2.779  35.280
sesameQC_plotHeatSNPs        27.894  1.740  30.971
KYCG_plotMeta                24.311  1.325  29.215
KYCG_plotEnrichAll           22.427  1.856  32.358
ELBAR                        22.203  0.942  24.306
matchDesign                  20.962  0.522  22.638
inferSpecies                 19.014  1.828  24.291
sesameQC_plotBetaByDesign    18.425  0.941  19.424
compareMouseStrainReference  17.339  0.922  20.524
compareReference             16.065  1.050  19.353
testEnrichmentSEA            15.955  0.543  19.858
KYCG_annoProbes              15.211  1.066  19.642
diffRefSet                   14.707  1.018  19.710
convertTo                    14.340  0.957  17.706
sesameQC_plotBar             13.786  0.614  16.794
getRefSet                    13.360  0.871  16.544
inferTissue                  12.608  0.997  17.068
KYCG_plotMetaEnrichment      11.604  0.801  16.878
DMR                          11.368  0.662  14.391
KYCG_buildGeneDBs            11.136  0.881  16.448
visualizeGene                11.271  0.259  14.826
inferStrain                  10.317  0.718  13.464
getSexInfo                    9.967  0.688  14.677
KYCG_plotSetEnrichment        9.261  0.870  12.476
dbStats                       8.965  1.046  12.478
sdf_read_table                8.898  1.022  12.275
DML                           9.166  0.614  12.150
dyeBiasNL                     8.588  0.586  10.292
createUCSCtrack               8.219  0.650  11.268
deidentify                    8.002  0.546  10.792
estimateLeukocyte             7.794  0.520  10.602
openSesame                    6.805  0.977  10.034
testEnrichment                6.674  1.037  11.069
reIdentify                    6.710  0.558   8.842
dyeBiasCorrMostBalanced       6.803  0.384   9.504
probeSuccessRate              6.671  0.318  10.422
scrubSoft                     6.586  0.319   6.919
inferSex                      5.782  0.415   8.404
inferSexKaryotypes            5.464  0.663   7.253
getMask                       5.523  0.538   9.390
sesameQC_rankStats            5.511  0.312   8.200
prepSesame                    5.387  0.303   6.918
bisConversionControl          4.681  0.239   7.209
visualizeProbes               4.784  0.052   5.962
parseGEOsignalMU              4.072  0.351   5.547
mapToMammal40                 4.011  0.303   6.634
qualityMask                   3.735  0.252   6.207
sesame-package                3.356  0.562   5.030
checkLevels                   3.531  0.347   5.103
summaryExtractTest            3.626  0.234   6.098
meanIntensity                 3.470  0.319   6.415
dyeBiasCorr                   3.502  0.195   5.920
print.DMLSummary              3.294  0.395   6.115
totalIntensities              3.416  0.096   5.997
updateSigDF                   3.259  0.144   5.629
KYCG_getDBs                   3.106  0.280   5.711
getAFTypeIbySumAlleles        2.236  0.164   5.013
* 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 ...
  ‘KYCG.Rmd’ using ‘UTF-8’... OK
  ‘QC.Rmd’ using ‘UTF-8’... OK
  ‘inferences.Rmd’ using ‘UTF-8’... OK
  ‘modeling.Rmd’ using ‘UTF-8’... OK
  ‘nonhuman.Rmd’ using ‘UTF-8’... OK
  ‘sesame.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-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-unknown-linux-gnu (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 
 23.560   1.318  27.178