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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --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 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* 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            38.931  0.797  39.731
imputeBetasByGenomicNeighbors 30.901  0.547  31.449
inferSex                      21.216  0.139  21.356
KYCG_plotMeta                 18.609  0.172  18.784
sesameQC_calcStats            17.257  0.212  17.471
imputeBetas                   16.728  0.479  17.208
KYCG_plotEnrichAll            16.648  0.517  17.168
sesameQC_plotHeatSNPs         15.496  0.068  15.566
inferSpecies                  13.506  0.625  14.133
ELBAR                         12.831  0.433  13.264
diffRefSet                    12.646  0.206  12.853
KYCG_annoProbes               11.258  0.179  11.439
sesameQC_plotBar              10.884  0.202  11.085
matchDesign                   10.712  0.044  10.762
KYCG_plotMetaEnrichment       10.436  0.191  10.628
getRefSet                     10.496  0.057  10.554
compareMouseStrainReference   10.280  0.081  10.363
compareReference               9.778  0.174   9.952
sesameQC_plotBetaByDesign      9.583  0.130   9.715
testEnrichmentSEA              8.995  0.344   9.339
KYCG_buildGeneDBs              9.045  0.270   9.319
visualizeGene                  8.821  0.137   8.958
inferTissue                    8.288  0.182   8.472
estimateLeukocyte              7.330  0.104   7.436
sdf_read_table                 7.326  0.099   7.425
inferStrain                    6.933  0.339   7.275
DMR                            6.876  0.210   7.087
DML                            6.724  0.296   7.020
dyeBiasNL                      6.128  0.060   6.190
getMask                        6.040  0.107   6.147
dbStats                        5.742  0.201   5.946
dyeBiasCorrMostBalanced        5.540  0.120   5.660
createUCSCtrack                5.227  0.082   5.354
testEnrichment                 5.097  0.084   5.181
deidentify                     4.993  0.063   5.058
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL sesame
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* installing to library ‘/home/biocbuild/bbs-3.20-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 version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
 18.538   1.729  20.255