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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings sesame_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    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 ‘1.24.0’
* 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
imputeBetasByGenomicNeighbors 45.179  0.896  46.273
testEnrichmentGene            43.282  0.799  44.170
sesameQC_calcStats            29.932  0.441  30.487
inferSex                      28.614  0.379  29.092
imputeBetas                   28.020  0.536  28.793
KYCG_plotMeta                 25.742  0.219  26.008
sesameQC_plotHeatSNPs         23.650  0.200  23.889
ELBAR                         21.594  0.303  21.933
KYCG_plotEnrichAll            20.937  0.480  21.463
inferSpecies                  18.408  0.780  19.267
sesameQC_plotBetaByDesign     18.637  0.206  18.900
matchDesign                   17.485  0.259  17.817
compareMouseStrainReference   16.161  0.112  16.307
compareReference              14.696  0.243  14.966
KYCG_annoProbes               14.021  0.204  14.246
diffRefSet                    13.839  0.168  14.042
KYCG_plotMetaEnrichment       12.812  0.160  12.993
testEnrichmentSEA             12.820  0.116  12.958
sesameQC_plotBar              12.575  0.319  12.959
getRefSet                     12.105  0.139  12.291
KYCG_buildGeneDBs             10.831  0.240  11.088
inferStrain                    9.916  0.323  10.274
visualizeGene                  9.801  0.200  10.019
DML                            9.539  0.259   9.820
DMR                            9.388  0.140   9.548
estimateLeukocyte              8.860  0.176   9.060
sdf_read_table                 8.757  0.155   8.946
dyeBiasNL                      8.698  0.044   8.761
inferTissue                    8.551  0.155   8.738
dbStats                        8.358  0.128   8.505
getMask                        7.493  0.172   7.688
KYCG_plotSetEnrichment         7.434  0.123   7.572
deidentify                     7.307  0.091   7.421
openSesame                     6.706  0.160   6.956
scrubSoft                      6.449  0.111   6.585
createUCSCtrack                6.345  0.160   6.525
probeSuccessRate               6.193  0.171   6.394
dyeBiasCorrMostBalanced        6.077  0.091   6.188
reIdentify                     6.007  0.083   6.111
testEnrichment                 5.896  0.151   6.060
sesameQC_rankStats             5.173  0.072   5.258
* 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/bin/R CMD INSTALL sesame
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
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, saveRDS, 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 
 22.280   0.739  22.955