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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings coMethDMR_1.10.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/coMethDMR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘coMethDMR/DESCRIPTION’ ... OK
* this is package ‘coMethDMR’ version ‘1.10.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘coMethDMR’ 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 ... NOTE
File ‘coMethDMR/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("Checking for cached SeSAMe data.")
    packageStartupMessage("Caching SeSAMe data for 450k/EPIC arrays.")

See section ‘Good practice’ in '?.onAttach'.
* checking Rd files ... NOTE
checkRd: (-1) AnnotateResults.Rd:13: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AnnotateResults.Rd:14: Lost braces in \itemize; meant \describe ?
checkRd: (-1) AnnotateResults.Rd:15: Lost braces in \itemize; meant \describe ?
checkRd: (-1) CoMethSingleRegion.Rd:55-60: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CoMethSingleRegion.Rd:61-63: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) CreateRdrop.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:45-46: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkComethylatedCpGs.Rd:48-49: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:25-26: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
checkRd: (-1) MarkMissing.Rd:29-30: Lost braces in \itemize; \value handles \item{}{} directly
* 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
CoMethSingleRegion  29.589  2.244  32.977
lmmTest             25.451  2.219  28.641
CpGsInfoOneRegion   18.161  1.510  20.373
SplitCpGDFbyRegion  17.050  0.907  18.692
lmmTestAllRegions   16.503  0.982  17.946
CoMethAllRegions    11.749  1.087  13.069
GetCpGsInRegion     11.426  0.604  12.498
AnnotateResults     10.658  1.052  11.711
CpGsInfoAllRegions   6.699  0.501   7.520
CloseBySingleRegion  6.497  0.561   7.322
CreateOutputDF       6.430  0.504   7.163
OrderCpGsByLocation  5.616  0.371   6.214
ImportSesameData     5.259  0.201   5.719
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL coMethDMR
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘coMethDMR’ ...
** using staged installation
** R
** data
** 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 (coMethDMR)

R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 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(coMethDMR)
Checking for cached SeSAMe data.
> 
> test_check("coMethDMR")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 12 ]
> 
> proc.time()
   user  system elapsed 
 57.417   3.247  61.837