Error in re-building vignettes:
  ...
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
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Retrieving data for taxon 'Allenopithecus_nigroviridis'

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Retrieving data for taxon 'Allocebus_trichotis'

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Retrieving data for taxon 'Alouatta_belzebul'

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Retrieving data for taxon 'Alouatta_caraya'

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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
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Retrieving data for taxon 'Alouatta_fusca'

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Retrieving data for taxon 'Alouatta_palliata'

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Retrieving data for taxon 'Alouatta_pigra'

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Retrieving data for taxon 'Alouatta_sara'

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Retrieving data for taxon 'Alouatta_seniculus'

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Retrieving data for taxon 'Aotus_azarai'

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Retrieving data for taxon 'Aotus_brumbacki'

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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
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Retrieving data for taxon 'Aotus_infulatus'

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Retrieving data for taxon 'Aotus_lemurinus'

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Retrieving data for taxon 'Aotus_miconax'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Aotus_miconax not found. Consider checking the spelling or alternate classification
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Retrieving data for taxon 'Aotus_nancymaae'

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Retrieving data for taxon 'Aotus_nigriceps'

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Retrieving data for taxon 'Aotus_trivirgatus'

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Retrieving data for taxon 'Aotus_vociferans'

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Retrieving data for taxon 'Arctocebus_aureus'

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Retrieving data for taxon 'Arctocebus_calabarensis'

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Retrieving data for taxon 'Ateles_belzebuth'

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Retrieving data for taxon 'Ateles_chamek'

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Retrieving data for taxon 'Ateles_fusciceps'

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Retrieving data for taxon 'Ateles_geoffroyi'

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Retrieving data for taxon 'Ateles_marginatus'

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Retrieving data for taxon 'Ateles_paniscus'

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Retrieving data for taxon 'Avahi_laniger'

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Retrieving data for taxon 'Brachyteles_arachnoides'

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Retrieving data for taxon 'Cacajao_calvus'

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Retrieving data for taxon 'Cacajao_melanocephalus'

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Retrieving data for taxon 'Callicebus_brunneus'

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Retrieving data for taxon 'Callicebus_caligatus'

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Retrieving data for taxon 'Callicebus_cinerascens'

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Retrieving data for taxon 'Callicebus_cupreus'

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Retrieving data for taxon 'Callicebus_donacophilus'

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Retrieving data for taxon 'Callicebus_dubius'

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Retrieving data for taxon 'Callicebus_hoffmannsi'

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Retrieving data for taxon 'Callicebus_modestus'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Callicebus_modestus not found. Consider checking the spelling or alternate classification
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Retrieving data for taxon 'Callicebus_moloch'

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Retrieving data for taxon 'Callicebus_oenanthe'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Callicebus_oenanthe not found. Consider checking the spelling or alternate classification
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Retrieving data for taxon 'Callicebus_olallae'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Callicebus_olallae not found. Consider checking the spelling or alternate classification
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Retrieving data for taxon 'Callicebus_personatus'

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Retrieving data for taxon 'Callicebus_torquatus'

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Retrieving data for taxon 'Callimico_goeldii'

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Retrieving data for taxon 'Callithrix_argentata'

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Retrieving data for taxon 'Callithrix_aurita'

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Retrieving data for taxon 'Callithrix_flaviceps'

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Retrieving data for taxon 'Callithrix_geoffroyi'

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Retrieving data for taxon 'Callithrix_humeralifera'

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Retrieving data for taxon 'Callithrix_jacchus'

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Retrieving data for taxon 'Callithrix_kuhlii'

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Retrieving data for taxon 'Callithrix_penicillata'

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Retrieving data for taxon 'Callithrix_pygmaea'

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Retrieving data for taxon 'Cebus_albifrons'

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Retrieving data for taxon 'Cebus_apella'

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Retrieving data for taxon 'Cebus_capucinus'

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Retrieving data for taxon 'Cebus_olivaceus'

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Retrieving data for taxon 'Cercocebus_agilis'

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Retrieving data for taxon 'Cercocebus_galeritus'

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Retrieving data for taxon 'Cercocebus_torquatus'

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Retrieving data for taxon 'Cercopithecus_ascanius'

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Retrieving data for taxon 'Cercopithecus_campbelli'

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Retrieving data for taxon 'Cercopithecus_cephus'

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Retrieving data for taxon 'Cercopithecus_diana'

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Retrieving data for taxon 'Cercopithecus_dryas'

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Retrieving data for taxon 'Cercopithecus_erythrogaster'

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Retrieving data for taxon 'Cercopithecus_erythrotis'

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Retrieving data for taxon 'Cercopithecus_hamlyni'

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Retrieving data for taxon 'Cercopithecus_lhoesti'

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Retrieving data for taxon 'Cercopithecus_mitis'

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Retrieving data for taxon 'Cercopithecus_mona'

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Retrieving data for taxon 'Cercopithecus_neglectus'

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Retrieving data for taxon 'Cercopithecus_nictitans'

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Retrieving data for taxon 'Cercopithecus_petaurista'

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Retrieving data for taxon 'Cercopithecus_pogonias'

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Retrieving data for taxon 'Cercopithecus_preussi'

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Retrieving data for taxon 'Cercopithecus_sclateri'

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Retrieving data for taxon 'Cercopithecus_solatus'

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Retrieving data for taxon 'Cercopithecus_wolfi'

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Retrieving data for taxon 'Cheirogaleus_major'

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Retrieving data for taxon 'Cheirogaleus_medius'

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Retrieving data for taxon 'Chiropotes_albinasus'

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Retrieving data for taxon 'Chiropotes_satanas'

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Retrieving data for taxon 'Chlorocebus_aethiops'

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Retrieving data for taxon 'Colobus_angolensis'

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Retrieving data for taxon 'Colobus_guereza'

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Retrieving data for taxon 'Colobus_polykomos'

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Retrieving data for taxon 'Colobus_satanas'

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Retrieving data for taxon 'Daubentonia_madagascariensis'

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Retrieving data for taxon 'Erythrocebus_patas'

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Retrieving data for taxon 'Eulemur_coronatus'

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Retrieving data for taxon 'Eulemur_fulvus'

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Retrieving data for taxon 'Eulemur_macaco'

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Retrieving data for taxon 'Eulemur_mongoz'

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Retrieving data for taxon 'Eulemur_rubriventer'

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Retrieving data for taxon 'Euoticus_elegantulus'

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Retrieving data for taxon 'Euoticus_pallidus'

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

Retrieving data for taxon 'Galago_alleni'

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Retrieving data for taxon 'Galago_gallarum'

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 'Galago_matschiei'

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 'Galago_moholi'

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 'Galago_senegalensis'

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 'Galagoides_demidoff'

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 'Galagoides_zanzibaricus'

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 'Gorilla_gorilla'

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 'Hapalemur_aureus'

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 'Hapalemur_griseus'

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 'Hapalemur_simus'

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 'Homo_sapiens'

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 'Hylobates_agilis'

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 'Hylobates_concolor'

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 'Hylobates_gabriellae'

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 'Hylobates_hoolock'

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 'Hylobates_klossii'

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 'Hylobates_lar'

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 'Hylobates_leucogenys'

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 'Hylobates_moloch'

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 'Hylobates_muelleri'

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

Retrieving data for taxon 'Hylobates_pileatus'

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 'Hylobates_syndactylus'

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 'Indri_indri'

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 'Lagothrix_flavicauda'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Lagothrix_flavicauda 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 'Lagothrix_lagotricha'

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 'Lemur_catta'

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 'Leontopithecus_caissara'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Leontopithecus_caissara 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 'Leontopithecus_chrysomela'

Not found. Consider checking the spelling or alternate classification
Warning in taxize_nexml(.) :
  ID for otu Leontopithecus_chrysomela 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 'Leontopithecus_chrysopygus'

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 'Leontopithecus_rosalia'

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 'Lepilemur_dorsalis'

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 'Lepilemur_edwardsi'

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 'Lepilemur_leucopus'

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 'Lepilemur_microdon'

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 'Lepilemur_mustelinus'

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 'Lepilemur_ruficaudatus'

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 'Lepilemur_septentrionalis'

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 'Lophocebus_albigena'

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 'Loris_tardigradus'

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 'Macaca_arctoides'

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 'Macaca_assamensis'

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 'Macaca_cyclopis'

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 'Macaca_fascicularis'

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

Retrieving data for taxon 'Macaca_fuscata'

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 'Macaca_maura'

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 'Macaca_mulatta'

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 'Macaca_nemestrina'

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 'Macaca_nigra'

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 'Macaca_ochreata'

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

Retrieving data for taxon 'Macaca_radiata'

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 'Macaca_silenus'

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

Retrieving data for taxon 'Macaca_sinica'

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 'Macaca_sylvanus'

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 'Macaca_thibetana'

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

Retrieving data for taxon 'Macaca_tonkeana'

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 'Mandrillus_leucophaeus'

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 'Mandrillus_sphinx'

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 'Microcebus_coquereli'

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 'Microcebus_murinus'

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 'Microcebus_rufus'

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 'Miopithecus_talapoin'

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 'Nasalis_concolor'

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 'Nasalis_larvatus'

Quitting from lines 205-209 (metadata.Rmd) 
Error: processing vignette ‘metadata.Rmd’ failed with diagnostics:
Start tag expected, '<' not found [4]
Execution halted