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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings sesame_1.17.7.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.17.7’
* 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
KYCG_plotEnrichAll          25.250  2.621  29.242
sesameQC_plotHeatSNPs       21.052  1.660  22.946
sesameQC_calcStats          19.553  1.502  21.235
inferSpecies                17.449  1.775  19.643
sesameQC_plotBar            14.082  1.216  15.772
matchDesign                 14.273  0.873  15.416
KYCG_plotMeta               12.412  0.905  14.189
diffRefSet                  11.452  1.260  13.063
compareMouseStrainReference 11.801  0.580  12.732
ELBAR                       12.069  0.276  12.516
sesameQC_plotBetaByDesign   10.945  0.719  11.664
compareReference            10.368  1.128  11.840
visualizeGene               10.248  0.943  11.701
testEnrichmentSEA           10.194  0.883  12.065
KYCG_annoProbes             10.047  1.016  12.200
getRefSet                    9.977  0.815  11.129
inferTissue                  9.761  0.976  11.874
KYCG_plotMetaEnrichment      9.237  0.782  10.586
KYCG_buildGeneDBs            8.844  0.728   9.918
getSexInfo                   8.527  0.576   9.401
inferStrain                  7.828  0.860   9.031
dyeBiasNL                    7.689  0.739   8.601
DML                          7.316  0.495   8.151
DMR                          7.463  0.228   8.037
testEnrichment               6.847  0.632   8.141
dbStats                      6.397  1.040   7.773
sdf_read_table               6.991  0.336   8.083
estimateLeukocyte            6.582  0.660   7.729
aggregateTestEnrichments     6.817  0.368   8.730
KYCG_plotSetEnrichment       6.569  0.504   7.838
probeSuccessRate             5.758  0.412   6.679
dyeBiasCorrMostBalanced      5.640  0.456   6.437
visualizeProbes              5.233  0.596   5.996
updateSigDF                  5.213  0.590   6.164
openSesame                   5.092  0.664   7.993
createUCSCtrack              5.223  0.420   6.137
inferSex                     4.990  0.547   5.880
reIdentify                   4.307  1.140   5.936
mapToMammal40                4.705  0.407   5.466
deidentify                   4.571  0.487   5.654
sesameQC_rankStats           4.234  0.619   5.198
meanIntensity                4.345  0.440   5.122
* 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-3.17-bioc/R/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
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 
 21.376   1.496  23.216