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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:DMRcate.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings DMRcate_3.1.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/DMRcate.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* 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 ‘3.1.2’
* 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 ... 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 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     167.126 10.522 192.222
DMR.plot            144.087  6.511 164.993
cpg.annotate         80.672  4.084  85.431
sequencing.annotate  58.661 10.134  70.758
rmPosReps            51.773  4.192  66.377
rmSNPandCH           50.795  4.511  64.410
dmrcate              43.049  3.488  46.874
extractRanges        38.134  1.544  40.296
* 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 117-121 [cpg.annotate] (EPICv2.Rnw)
Error: processing vignette 'EPICv2.Rnw' failed with diagnostics:
cannot subset by character when names are NULL
--- 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
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/DMRcate.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL DMRcate
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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)