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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_1.22.0.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 ‘1.22.0’
* 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          124.283  1.794 147.918
inferSex                     43.156  0.479  48.005
sesameQC_calcStats           30.170  0.195  31.491
KYCG_plotMeta                25.626  0.634  29.540
sesameQC_plotHeatSNPs        26.010  0.171  27.298
ELBAR                        23.494  0.268  24.883
KYCG_plotEnrichAll           21.476  0.379  29.534
inferSpecies                 19.458  0.543  23.253
matchDesign                  17.937  0.319  19.364
sesameQC_plotBetaByDesign    17.514  0.120  17.664
compareMouseStrainReference  16.593  0.319  19.102
KYCG_annoProbes              16.330  0.352  20.140
diffRefSet                   16.210  0.280  18.666
compareReference             15.070  0.276  17.512
KYCG_plotMetaEnrichment      13.404  0.434  17.097
sesameQC_plotBar             13.581  0.204  15.960
testEnrichmentSEA            12.610  0.196  16.253
getRefSet                    12.576  0.176  14.911
KYCG_buildGeneDBs            12.003  0.291  14.466
visualizeGene                10.948  0.172  14.366
DMR                          10.790  0.275  13.332
inferStrain                  10.442  0.212  12.819
dyeBiasNL                     9.910  0.104  11.100
dbStats                       9.333  0.276  11.772
DML                           8.791  0.458  11.625
inferTissue                   8.745  0.252  11.182
sdf_read_table                8.789  0.128  11.074
estimateLeukocyte             7.987  0.196  10.355
KYCG_plotSetEnrichment        7.832  0.261  10.327
deidentify                    7.538  0.148   9.887
openSesame                    6.926  0.379   9.475
createUCSCtrack               6.946  0.139   9.271
probeSuccessRate              6.743  0.200  10.174
testEnrichment                6.487  0.191   9.910
scrubSoft                     6.515  0.060   6.586
reIdentify                    6.431  0.128   7.649
dyeBiasCorrMostBalanced       6.336  0.083   8.688
getMask                       5.557  0.132   8.935
bisConversionControl          5.234  0.123   7.523
prepSesame                    4.888  0.196   6.165
sesameQC_rankStats            4.986  0.080   7.234
print.DMLSummary              3.939  0.246   6.359
parseGEOsignalMU              3.835  0.156   5.067
mapToMammal40                 3.922  0.068   6.149
checkLevels                   3.770  0.200   5.054
dyeBiasCorr                   3.729  0.072   6.055
qualityMask                   3.692  0.108   5.953
totalIntensities              3.500  0.079   5.737
meanIntensity                 3.369  0.087   5.631
summaryExtractTest            3.238  0.100   5.489
sesameQC_plotIntensVsBetas    3.281  0.036   6.852
updateSigDF                   3.162  0.092   5.418
KYCG_getDBs                   3.127  0.091   5.978
* 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 
 23.121   1.766  27.167