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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data metagenomeFeatures
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* checking for file ‘metagenomeFeatures/DESCRIPTION’ ... OK
* preparing ‘metagenomeFeatures’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘MgDb_and_mgFeatures_classes.Rmd’ using rmarkdown
Quitting from lines 58-63 (MgDb_and_mgFeatures_classes.Rmd) 
Error: processing vignette 'MgDb_and_mgFeatures_classes.Rmd' failed with diagnostics:
no applicable method for 'select_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
--- failed re-building ‘MgDb_and_mgFeatures_classes.Rmd’

--- re-building ‘database-explore.Rmd’ using rmarkdown
Warning: `filter_()` was deprecated in dplyr 0.7.0.
Please use `filter()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
Quitting from lines 62-68 (database-explore.Rmd) 
Error: processing vignette 'database-explore.Rmd' failed with diagnostics:
no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
--- failed re-building ‘database-explore.Rmd’

--- re-building ‘retrieve-feature-data.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
Found more than one class "phylo" in cache; using the first, from namespace 'metagenomeFeatures'
Also defined by 'tidytree' 'phyloseq'
Found more than one class "phylo" in cache; using the first, from namespace 'metagenomeFeatures'
Also defined by 'tidytree' 'phyloseq'
Found more than one class "phylo" in cache; using the first, from namespace 'metagenomeFeatures'
Also defined by 'tidytree' 'phyloseq'
Found more than one class "phylo" in cache; using the first, from namespace 'metagenomeFeatures'
Also defined by 'tidytree' 'phyloseq'
Quitting from lines 88-98 (retrieve-feature-data.Rmd) 
Error: processing vignette 'retrieve-feature-data.Rmd' failed with diagnostics:
no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
--- failed re-building ‘retrieve-feature-data.Rmd’

SUMMARY: processing the following files failed:
  ‘MgDb_and_mgFeatures_classes.Rmd’ ‘database-explore.Rmd’
  ‘retrieve-feature-data.Rmd’

Error: Vignette re-building failed.
Execution halted