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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:sesame.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings sesame_1.22.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/sesame.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘sesame/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘sesame’ version ‘1.22.1’
* 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            102.525  7.593 113.479
imputeBetasByGenomicNeighbors  32.758  1.520  34.751
KYCG_plotMeta                  23.297  1.659  25.439
KYCG_plotEnrichAll             21.090  2.296  24.542
inferSex                       21.605  1.123  23.043
imputeBetas                    18.710  1.572  20.796
sesameQC_calcStats             18.680  1.188  20.025
inferSpecies                   16.250  2.016  18.805
ELBAR                          16.629  1.072  17.877
KYCG_annoProbes                15.435  1.408  17.379
sesameQC_plotHeatSNPs          16.288  0.528  16.974
diffRefSet                     13.392  1.308  15.016
compareMouseStrainReference    11.693  1.065  13.116
matchDesign                    11.497  0.907  12.562
compareReference               11.199  1.179  12.694
getRefSet                      11.511  0.784  12.651
KYCG_buildGeneDBs              11.168  0.896  12.382
KYCG_plotMetaEnrichment        10.688  1.036  12.200
sesameQC_plotBar               10.816  0.400  11.671
testEnrichmentSEA               9.908  0.969  11.390
visualizeGene                   8.889  0.844  10.242
DMR                             8.865  0.588   9.811
sesameQC_plotBetaByDesign       9.053  0.352   9.405
sdf_read_table                  8.629  0.524   9.491
estimateLeukocyte               7.915  0.804   9.037
inferStrain                     7.301  0.651   8.267
inferTissue                     6.897  0.952   8.179
dbStats                         6.893  0.800   8.072
getMask                         6.516  0.708   7.857
DML                             6.692  0.381   7.438
dyeBiasNL                       6.058  0.544   6.760
updateSigDF                     5.780  0.808   6.907
createUCSCtrack                 6.080  0.420   6.815
deidentify                      5.809  0.528   6.705
dyeBiasCorrMostBalanced         5.892  0.408   6.652
testEnrichment                  5.273  0.799   6.546
KYCG_plotSetEnrichment          5.298  0.471   6.092
probeSuccessRate                5.040  0.439   5.985
openSesame                      4.837  0.395   5.600
bisConversionControl            4.384  0.376   5.120
* 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:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL sesame
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* installing to library ‘/home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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, 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 
 19.388   0.963  20.656