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### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings sesame_1.21.15.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* 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
* using option ‘--no-vignettes’
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.21.15’
* 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 code 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 whether 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          131.803  2.169 157.215
inferSex                     46.884  0.738  52.055
sesameQC_calcStats           31.702  0.168  33.000
KYCG_plotMeta                27.874  0.240  31.616
sesameQC_plotHeatSNPs        26.211  0.271  30.658
ELBAR                        25.695  0.415  27.241
KYCG_plotEnrichAll           23.732  0.605  31.916
sesameQC_plotBetaByDesign    19.111  0.120  19.272
inferSpecies                 18.504  0.479  22.246
matchDesign                  18.745  0.228  20.081
KYCG_annoProbes              17.781  0.367  22.195
compareMouseStrainReference  17.687  0.295  20.172
diffRefSet                   17.645  0.323  20.144
compareReference             16.080  0.307  18.561
KYCG_plotMetaEnrichment      14.325  0.701  18.274
getRefSet                    14.109  0.219  16.499
sesameQC_plotBar             13.662  0.160  16.000
testEnrichmentSEA            13.572  0.223  17.158
KYCG_buildGeneDBs            13.215  0.310  15.820
DMR                          12.088  0.439  14.695
visualizeGene                11.826  0.215  15.393
inferStrain                  11.249  0.284  13.713
dyeBiasNL                    11.361  0.076  13.051
dbStats                      10.773  0.343  13.306
DML                          10.173  0.431  12.986
sdf_read_table                9.249  0.131  11.544
estimateLeukocyte             9.067  0.192  11.475
inferTissue                   8.811  0.250  11.235
KYCG_plotSetEnrichment        8.492  0.383  11.073
deidentify                    8.243  0.152  10.593
createUCSCtrack               7.970  0.183  10.312
dyeBiasCorrMostBalanced       7.131  0.159   9.459
openSesame                    7.001  0.168   9.339
scrubSoft                     7.059  0.000   7.074
probeSuccessRate              6.551  0.108   9.874
reIdentify                    6.483  0.056   7.630
getMask                       6.271  0.172   9.662
testEnrichment                5.848  0.092   9.164
sesameQC_rankStats            5.712  0.067   7.927
bisConversionControl          5.589  0.178   7.921
prepSesame                    4.993  0.051   6.123
dyeBiasL                      4.490  0.072   5.637
mapToMammal40                 4.264  0.075   6.503
checkLevels                   4.034  0.199   5.345
dyeBiasCorr                   4.067  0.084   6.294
parseGEOsignalMU              3.912  0.088   5.187
totalIntensities              3.919  0.052   6.224
qualityMask                   3.780  0.060   6.017
print.DMLSummary              3.661  0.080   5.881
updateSigDF                   3.576  0.080   7.404
summaryExtractTest            3.410  0.044   5.603
meanIntensity                 3.259  0.120   5.538
KYCG_getDBs                   3.206  0.072   5.425
KYCG_plotPointRange           3.013  0.209   9.054
getAFTypeIbySumAlleles        2.875  0.083   5.111
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

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###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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, 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 5 ]
> 
> proc.time()
   user  system elapsed 
 23.671   2.489  28.458