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### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings sesame_1.16.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/sesame.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.16.1’
* 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 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
KYCG_plotEnrichAll          31.667  0.684  34.091
sesameQC_calcStats          23.017  0.168  23.440
sesameQC_plotHeatSNPs       21.677  0.260  22.193
KYCG_plotMeta               20.634  0.232  21.556
inferSpecies                17.031  0.800  18.421
DMR                         16.724  0.376  17.781
diffRefSet                  14.199  0.288  14.851
sesameQC_plotBetaByDesign   13.780  0.280  14.061
matchDesign                 13.528  0.352  14.048
compareMouseStrainReference 13.032  0.176  13.648
KYCG_annoProbes             12.709  0.400  13.704
KYCG_plotMetaEnrichment     12.732  0.204  13.572
sesameQC_plotBar            12.047  0.236  12.796
compareReference            11.787  0.272  12.479
KYCG_buildGeneDBs           11.358  0.355  12.224
testEnrichment              11.068  0.296  12.396
getRefSet                   10.710  0.152  11.289
testEnrichmentSEA           10.576  0.180  11.450
sdf_read_table              10.174  0.140  10.651
inferTissue                 10.013  0.208  10.815
detectionIB                  9.814  0.156  10.140
visualizeGene                9.529  0.268  10.392
getSexInfo                   9.547  0.172  10.414
dbStats                      8.611  0.304   9.423
DML                          7.925  0.408   8.762
inferStrain                  7.582  0.356   8.445
createUCSCtrack              7.505  0.200   8.123
estimateLeukocyte            7.164  0.144   7.833
dyeBiasNL                    6.717  0.140   7.110
dyeBiasCorrMostBalanced      6.045  0.104   6.678
probeSuccessRate             5.983  0.132   6.895
deidentify                   6.043  0.056   6.609
KYCG_plotSetEnrichment       5.836  0.088   6.460
openSesame                   5.338  0.152   5.998
reIdentify                   5.052  0.040   5.349
bisConversionControl         4.973  0.088   5.480
updateSigDF                  4.642  0.152   5.216
* 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/bbs-3.16-bioc/R/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 21.483   0.963  22.850