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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:sesame.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings sesame_1.18.4.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck'
* using R version 4.3.1 (2023-06-16 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.2.0
    GNU Fortran (GCC) 12.2.0
* 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 '1.18.4'
* 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 ... WARNING
'::' or ':::' import not declared from: 'BiocManager'
* 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          111.25   5.04  183.88
sesameQC_calcStats           23.76   0.90   24.69
sesameQC_plotHeatSNPs        22.15   0.83   23.00
KYCG_plotEnrichAll           18.91   1.05   27.52
KYCG_plotMeta                17.87   0.61   21.83
matchDesign                  16.37   0.70   17.14
inferSpecies                 15.82   0.66   22.64
ELBAR                        13.19   1.45   17.09
sesameQC_plotBar             14.03   0.41   27.02
sdf_read_table               12.95   0.48   13.61
KYCG_annoProbes              12.69   0.64   16.31
compareMouseStrainReference  12.03   0.55   14.80
diffRefSet                   11.82   0.59   18.79
sesameQC_plotBetaByDesign    11.29   0.67   11.95
compareReference             10.70   0.50   11.37
KYCG_buildGeneDBs            10.71   0.25   17.31
KYCG_plotMetaEnrichment      10.10   0.74   10.88
getRefSet                    10.39   0.34   10.76
testEnrichmentSEA             9.92   0.64   10.76
inferTissue                   9.69   0.56   10.30
visualizeGene                 9.33   0.42    9.85
DML                           7.75   1.78   12.89
getSexInfo                    8.40   0.46    9.05
sdf_write_table               8.27   0.23    8.53
inferStrain                   7.45   0.67    8.18
DMR                           7.45   0.21    7.72
estimateLeukocyte             6.92   0.51   13.54
visualizeProbes               6.84   0.22    7.09
dbStats                       5.85   0.67   15.69
dyeBiasCorrMostBalanced       5.78   0.42   17.48
openSesame                    5.39   0.59    7.08
bisConversionControl          5.53   0.33   10.14
createUCSCtrack               5.22   0.36    8.99
testEnrichment                5.05   0.43    5.56
deidentify                    5.21   0.26    5.66
probeSuccessRate              5.06   0.39    5.53
KYCG_plotSetEnrichment        4.78   0.49    6.00
getMask                       4.78   0.41    5.94
dyeBiasNL                     4.48   0.19    5.04
updateSigDF                   3.48   0.22    5.82
checkLevels                   3.27   0.23    6.25
imputeTo                      1.49   0.21    5.23
* 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: 1 WARNING
See
  'F:/biocbuild/bbs-3.17-bioc/meat/sesame.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL sesame
###
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* installing to library 'F:/biocbuild/bbs-3.17-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 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 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 
  18.32    2.42   20.87