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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:coMethDMR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings coMethDMR_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/coMethDMR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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  40.866  1.288  48.122
lmmTest             37.216  1.087  42.874
CpGsInfoOneRegion   26.468  0.740  30.782
SplitCpGDFbyRegion  26.405  0.767  30.543
lmmTestAllRegions   22.684  0.680  25.629
GetCpGsInRegion     18.833  0.630  21.885
CoMethAllRegions    17.305  0.433  18.868
AnnotateResults     13.637  0.380  14.520
CpGsInfoAllRegions  11.478  0.307  12.946
CloseBySingleRegion 10.637  0.952  13.132
OrderCpGsByLocation  8.706  0.272  10.105
CreateOutputDF       7.764  0.234   9.168
ImportSesameData     6.800  0.222   8.131
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/coMethDMR.Rcheck/00check.log’
for details.