Error(s) in re-building vignettes:
--- re-building ‘S4.Rmd’ using rmarkdown
Loading required package: ape
--- finished re-building ‘S4.Rmd’

--- re-building ‘metadata.Rmd’ using rmarkdown
Loading required package: ape

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Allenopithecus_nigroviridis'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Allocebus_trichotis'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_belzebul'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_caraya'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_coibensis'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Alouatta_coibensis not found. Consider checking the spelling or alternate classification
No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_fusca'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_palliata'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_pigra'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_sara'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Alouatta_seniculus'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Aotus_azarai'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Aotus_brumbacki'

No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Aotus_hershkovitzi'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Aotus_hershkovitzi not found. Consider checking the spelling or alternate classification
No ENTREZ API key provided
 Get one via use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

Retrieving data for taxon 'Aotus_infulatus'

Quitting from lines 205-209 (metadata.Rmd) 
Error: processing vignette 'metadata.Rmd' failed with diagnostics:
'{"error":"API rate limit exceeded","api-key":"163.1.211.17","count":"5","limit":"3"}
' does not exist in current working directory ('/data/gannet/ripley/R/packages/tests-devel/RNeXML.Rcheck/vign_test/RNeXML/vignettes').
--- failed re-building ‘metadata.Rmd’

--- re-building ‘simmap.Rmd’ using rmarkdown
Loading required package: maps
--- finished re-building ‘simmap.Rmd’

--- re-building ‘sparql.Rmd’ using rmarkdown
Loading required package: ape
Loading required package: maps
--- finished re-building ‘sparql.Rmd’

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

Error: Vignette re-building failed.
Execution halted