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###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings sesame_1.20.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/sesame.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'sesame/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'sesame' version '1.20.0'
* 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 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 R 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 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          114.72   4.74  126.84
sesameQC_calcStats           27.14   0.88   28.03
sesameQC_plotHeatSNPs        26.79   1.01   27.84
KYCG_plotEnrichAll           19.89   1.34   22.51
KYCG_plotMeta                20.27   0.63   21.50
matchDesign                  18.61   0.69   19.33
inferSpecies                 17.39   0.70   18.92
ELBAR                        16.03   1.55   17.89
sdf_read_table               15.78   0.52   16.38
KYCG_annoProbes              14.53   0.95   15.89
testEnrichmentSEA            14.48   0.67   15.36
convertTo                    14.42   0.55   16.53
sesameQC_plotBar             13.80   0.30   14.15
inferTissue                  12.14   0.72   13.03
diffRefSet                   12.09   0.66   13.81
compareReference             11.96   0.50   12.51
compareMouseStrainReference  11.71   0.68   12.60
getRefSet                    12.00   0.39   12.46
sesameQC_plotBetaByDesign    11.61   0.69   12.30
KYCG_buildGeneDBs            11.50   0.54   12.69
DML                           9.18   1.88   11.16
KYCG_plotMetaEnrichment      10.25   0.59   10.94
visualizeGene                 9.52   0.45   10.03
inferStrain                   9.35   0.55    9.94
DMR                           8.86   0.37    9.42
dbStats                       8.54   0.67    9.64
getSexInfo                    8.72   0.42    9.34
sdf_write_table               8.50   0.21    8.77
createUCSCtrack               8.14   0.37    8.77
estimateLeukocyte             7.20   0.43    8.28
testEnrichment                6.84   0.59    7.52
openSesame                    6.45   0.56    7.13
deidentify                    6.53   0.36    7.06
dyeBiasNL                     6.30   0.29    6.61
KYCG_plotSetEnrichment        5.61   0.55    6.27
dyeBiasCorrMostBalanced       5.79   0.24    6.09
probeSuccessRate              5.60   0.36    6.04
inferSex                      5.31   0.39    5.77
bisConversionControl          5.05   0.25    5.82
getMask                       4.85   0.39    5.46
prepSesame                    4.68   0.32    5.02
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... 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:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL sesame
###
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* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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, sort, 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 1 ]
> 
> proc.time()
   user  system elapsed 
  21.95    2.73   24.84