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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:AHPubMedDbs.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings AHPubMedDbs_0.99.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.16-data-annotation/meat/AHPubMedDbs.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘AHPubMedDbs/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AHPubMedDbs’ version ‘0.99.8’
* 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 ‘AHPubMedDbs’ 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 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 Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘pubmed.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘pubmed.Rmd’ using rmarkdown
Quitting from lines 55-56 (pubmed.Rmd) 
Error: processing vignette 'pubmed.Rmd' failed with diagnostics:
error in evaluating the argument 'x' in selecting a method for function 'mcols': error reading from connection
--- failed re-building ‘pubmed.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.16-data-annotation/meat/AHPubMedDbs.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL AHPubMedDbs
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* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘AHPubMedDbs’ ...
** using staged installation
** inst
** 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 (AHPubMedDbs)