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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:dmrseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings dmrseq_1.19.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/dmrseq.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘dmrseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dmrseq’ version ‘1.19.1’
* 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 ‘dmrseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
* 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 R 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘dmrseq-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAnnot
> ### Title: Retrieve annotation information
> ### Aliases: getAnnot
> 
> ### ** Examples
> 
> 
> # get annotation information for hg19
> annoTrack <- getAnnot('hg19')
Building CpG islands...
loading from cache
Building CpG shores...
Building CpG shelves...
Building inter-CpG-islands...
Download of CpG annotation successful!
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (4 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (3 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (2 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Trying again (1 attempts remaining)
Error in get(txdb_name) : 
  object 'TxDb.Hsapiens.UCSC.hg19.knownGene' not found

Error in getAnnot("hg19") : Annotation could not be retrieved.
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘dmrseq.Rmd’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘dmrseq.Rmd’ using rmarkdown
Quitting from lines 543-548 (dmrseq.Rmd) 
Error: processing vignette 'dmrseq.Rmd' failed with diagnostics:
Annotation could not be retrieved.
--- failed re-building ‘dmrseq.Rmd’

SUMMARY: processing the following file failed:
  ‘dmrseq.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/dmrseq.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL dmrseq
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘dmrseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (dmrseq)