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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings sesame_1.23.6.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/sesame.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.23.6'
* 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 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 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            44.45   6.92   54.31
imputeBetasByGenomicNeighbors 35.79   2.79   39.82
inferSex                      26.78   1.93   28.76
sesameQC_calcStats            23.94   2.20   26.13
sesameQC_plotHeatSNPs         22.47   2.44   24.96
KYCG_plotMeta                 22.33   2.08   25.08
imputeBetas                   19.70   2.90   25.16
KYCG_plotEnrichAll            18.19   3.30   22.69
inferSpecies                  16.44   2.21   19.52
sdf_read_table                16.86   1.03   18.00
matchDesign                   16.02   1.25   17.36
DML                           11.12   6.12   31.49
ELBAR                         14.58   1.77   16.42
sesameQC_plotBar              14.80   1.19   16.86
KYCG_annoProbes               13.10   1.94   15.64
compareReference              12.19   2.85   15.25
diffRefSet                    12.68   1.23   14.71
sesameQC_plotBetaByDesign     12.27   1.52   13.75
visualizeGene                 11.76   1.63   13.69
getRefSet                     11.56   1.17   12.78
testEnrichmentSEA             10.66   1.98   12.80
KYCG_plotMetaEnrichment       11.09   1.40   12.70
compareMouseStrainReference   11.44   1.03   12.69
KYCG_buildGeneDBs             10.84   1.07   12.33
inferTissue                    8.00   2.92   11.08
sdf_write_table               10.17   0.35   10.54
inferStrain                    8.98   1.19   10.23
dbStats                        6.33   3.19   10.19
testEnrichment                 5.55   3.67    9.46
DMR                            7.97   0.68    8.94
estimateLeukocyte              7.22   1.21    8.84
getMask                        6.30   1.91    8.72
openSesame                     5.69   1.45    7.31
createUCSCtrack                5.81   1.22    7.26
probeSuccessRate               5.49   1.40    7.13
deidentify                     5.96   0.91    7.04
dyeBiasCorrMostBalanced        6.15   0.72    7.70
KYCG_plotSetEnrichment         5.55   1.03    6.69
dyeBiasNL                      5.72   0.48    6.24
prepSesame                     4.70   0.92    5.70
bisConversionControl           4.81   0.77    5.91
scrubSoft                      4.60   0.84    5.44
checkLevels                    2.80   2.22    5.27
* 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:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL sesame
###
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* installing to library 'F:/biocbuild/bbs-3.20-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 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 
  22.82   21.00   44.62