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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DMRcate_2.99.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DMRcate.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DMRcate/DESCRIPTION’ ... OK
* this is package ‘DMRcate’ version ‘2.99.4’
* 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 ‘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 loading without being on the library search path ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                       user system elapsed
DMRcate-package     157.884  9.258 181.279
DMR.plot            148.457  5.860 170.445
sequencing.annotate  80.664 17.332 146.462
cpg.annotate         88.433  2.704  91.751
rmPosReps            42.381  1.132  44.203
extractRanges        40.296  1.328  42.290
dmrcate              36.513  0.812  37.635
rmSNPandCH           29.972  1.148  31.674
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘EPICv1_and_450K.Rnw’ using knitr
--- finished re-building ‘EPICv1_and_450K.Rnw’

--- re-building ‘EPICv2.Rnw’ using knitr

Quitting from lines 134-138 [plot] (EPICv2.Rnw)
Error: processing vignette 'EPICv2.Rnw' failed with diagnostics:
Unable to query any Ensembl site
--- failed re-building ‘EPICv2.Rnw’

--- re-building ‘sequencing.Rnw’ using knitr
--- finished re-building ‘sequencing.Rnw’

SUMMARY: processing the following file failed:
  ‘EPICv2.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DMRcate.Rcheck/00check.log’
for details.