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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:DMRcate.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings DMRcate_2.99.5.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/DMRcate.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 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 'DMRcate/DESCRIPTION' ... OK
* this is package 'DMRcate' version '2.99.5'
* 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 'DMRcate' 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 ... NOTE
Problems with news in 'NEWS':
  Cannot process chunk/lines:
    DSS dependency removed
  Cannot process chunk/lines:
    CITATION updated.
  Cannot process chunk/lines:
    BUG FIXES
    •	annotate() renamed to cpg.annotate to avoid clashes with same-named function in ggplot2
  Cannot process chunk/lines:
    NEW FEATURES
    •	Kernel estimator has been rewritten from scratch without the need for ks:::kde. Now only takes moderated t-values as cpg weights, as required by the chi-square transformation. 
    •	Now allows for multi-level factor experiments, as allowed by limma. Contrasts should be specified with a contrast matrix, otherwise the design matrix MUST have an intercept. (Thanks to Tim Triche Jr. and David Martino for their advice).
    •	A GRanges object can be produced from the results.
    •	XY probes can also be filtered out using rmSNPandCH().
    •	DMR.plot() allows group median lines to be plotted to better visualise distances between groups (Thanks to Susan van Dijk and Magnus Tobiasson for their advice).
* 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...

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### Running command:
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###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL DMRcate
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* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'DMRcate' ...
** 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 (DMRcate)