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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 4.4.2 (2024-10-31)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 12.3.1 (openEuler 12.3.1-36.oe2403)
* running under: openEuler 24.03 (LTS)
* 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
testEnrichmentGene            43.148  0.714  43.977
imputeBetasByGenomicNeighbors 40.559  0.495  41.144
inferSex                      24.312  0.172  24.531
KYCG_plotMeta                 23.384  0.139  23.589
imputeBetas                   22.933  0.397  23.593
sesameQC_calcStats            22.601  0.124  22.790
sesameQC_plotHeatSNPs         20.282  0.171  20.507
KYCG_plotEnrichAll            19.552  0.475  20.103
inferSpecies                  16.088  0.491  16.616
matchDesign                   15.870  0.108  16.012
ELBAR                         15.719  0.160  15.924
compareMouseStrainReference   15.688  0.076  15.818
KYCG_annoProbes               13.425  0.227  13.694
compareReference              13.444  0.192  13.673
sesameQC_plotBetaByDesign     13.278  0.096  13.420
diffRefSet                    13.131  0.144  13.321
sesameQC_plotBar              12.062  0.163  12.263
KYCG_plotMetaEnrichment       11.924  0.220  12.178
testEnrichmentSEA             11.850  0.172  12.052
getRefSet                     11.482  0.171  11.689
KYCG_buildGeneDBs              9.999  0.260  10.300
visualizeGene                  9.531  0.171   9.722
DMR                            9.163  0.203   9.398
DML                            8.979  0.315   9.331
inferStrain                    8.107  0.263   8.395
sdf_read_table                 8.248  0.115   8.379
estimateLeukocyte              7.958  0.139   8.139
dbStats                        7.810  0.120   7.960
inferTissue                    7.283  0.307   7.611
KYCG_plotSetEnrichment         6.920  0.235   7.177
deidentify                     6.733  0.095   6.859
getMask                        6.553  0.147   6.729
dyeBiasNL                      6.633  0.048   6.702
dyeBiasCorrMostBalanced        6.174  0.092   6.290
createUCSCtrack                6.127  0.095   6.245
openSesame                     5.908  0.199   6.149
testEnrichment                 5.517  0.096   5.630
probeSuccessRate               5.443  0.152   5.607
reIdentify                     5.352  0.048   5.411
updateSigDF                    5.261  0.104   5.378
bisConversionControl           5.046  0.087   5.153
* 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-4.4.2/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 
 20.284   0.751  21.075