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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:coMethDMR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings coMethDMR_0.99.12.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/coMethDMR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'coMethDMR/DESCRIPTION' ... OK
* this is package 'coMethDMR' version '0.99.12'
* 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 'coMethDMR' can be installed ... WARNING
Found the following significant warnings:
  Note: possible error in 'sesameDataCache("HM450")': unused argument ("HM450") 
  Note: possible error in 'sesameDataCache("EPIC")': unused argument ("EPIC") 
See 'D:/biocbuild/bbs-3.15-bioc/meat/coMethDMR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
* 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 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 ... NOTE
File 'coMethDMR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("Checking for cached SeSAMe data.")
    packageStartupMessage("Caching SeSAMe data for 450k arrays.")
    packageStartupMessage("Caching SeSAMe data for EPIC arrays.")

See section 'Good practice' in '?.onAttach'.

.onLoad: possible error in sesameDataCache("HM450"): unused argument
  ("HM450")
.onLoad: possible error in sesameDataCache("EPIC"): unused argument
  ("EPIC")
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
AnnotateResults     8.25   0.92    9.17
lmmTestAllRegions   4.87   0.48    5.36
CloseBySingleRegion 4.86   0.27    6.10
* 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, 1 NOTE
See
  'D:/biocbuild/bbs-3.15-bioc/meat/coMethDMR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL coMethDMR
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'coMethDMR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'sesameDataCache("HM450")': unused argument ("HM450") 
Note: possible error in 'sesameDataCache("EPIC")': unused argument ("EPIC") 
** help
*** installing help indices
  converting help for package 'coMethDMR'
    finding HTML links ... done
    AnnotateResults                         html  
    CloseBySingleRegion                     html  
    CoMethAllRegions                        html  
    CoMethSingleRegion                      html  
    CpGsInfoAllRegions                      html  
    CpGsInfoOneRegion                       html  
    CreateOutputDF                          html  
    CreateParallelWorkers                   html  
    CreateRdrop                             html  
    FindComethylatedRegions                 html  
    GetCpGsInRegion                         html  
    GetResiduals                            html  
    MarkComethylatedCpGs                    html  
    NameRegion                              html  
    OrderCpGsByLocation                     html  
    RegionsToRanges                         html  
    SplitCpGDFbyRegion                      html  
    WriteCloseByAllRegions                  html  
    betaMatrix_ex1                          html  
    betaMatrix_ex2                          html  
    betaMatrix_ex3                          html  
    betaMatrix_ex4                          html  
    betasChr22_df                           html  
    coMethDMR_setup                         html  
    lmmTest                                 html  
    lmmTestAllRegions                       html  
    pheno_df                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
snapshotDate(): 2022-03-01
** testing if installed package can be loaded from final location
snapshotDate(): 2022-03-01
** testing if installed package keeps a record of temporary installation path
* DONE (coMethDMR)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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(coMethDMR)
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, 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.
Checking for cached SeSAMe data.
snapshotDate(): 2022-03-01
> 
> test_check("coMethDMR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
  24.00    1.93   27.48