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vijaybarve / bdvis

Biodiversity data Visualizations in R
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gettaxo does not work #98

Open vijaybarve opened 6 years ago

vijaybarve commented 6 years ago 
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/
Rishi0812 commented 4 years ago

Session Info.txt

Code: require(bdvis) require(rinat) inat <- get_inat_obs_project("reptileindia") inat <- format_bdvis(inat, source="rinat") inat <- gettaxo(inat)

Error : No ENTREZ API key provided Get one via taxize::use_entrez() See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ |=================================================| 100% Creating local database taxo.db ... Warning messages: 1: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery(). 2: In result_fetch(res@ptr, n = n) : SQL statements must be issued with dbExecute() or dbSendStatement() instead of dbGetQuery() or dbSendQuery().

hxxr commented 4 years ago

sessionInfo.txt

Code:

require(bdvis)
require(rinat)
inat <- get_inat_obs_project("reptileindia") 
inat <- format_bdvis(inat,source='rinat')

gettaxo(inat)

Error:

Local database taxo.db is absent
Processing names not present in local database ...
  |                                                                      |   0%No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
==  1 queries  ===============

Retrieving data for taxon 'Acrochordus granulatus'

v  Found:  Acrochordus+granulatus
==  Results  =================

* Total: 1
* Found: 1
* Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
  |                                                                      |   0%No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
==  1 queries  ===============

Retrieving data for taxon 'Agama'

v  Found:  Agama
==  Results  =================

* Total: 1
* Found: 1
* Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
  |                                                                      |   1%No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
==  1 queries  ===============

Retrieving data for taxon 'Agamidae'

v  Found:  Agamidae
==  Results  =================

* Total: 1
* Found: 1
* Not Found: 0
No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
  |=                                                                     |   1%No ENTREZ API key provided
 Get one via taxize::use_entrez()
See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
==  1 queries  ===============

Retrieving data for taxon 'Ahaetulla nasuta'

Error: '{"error":"API rate limit exceeded","api-key":"67.21.155.29","count":"4","limit":"3"}
' does not exist in current working directory ('C:/WINDOWS/system32').
In addition: Warning message:
package 'RSQLite' was built under R version 3.6.2
pratishrai commented 4 years ago

Code:

require(bdvis)
require(rinat)
inat<-get_inat_obs_project("reptileindia")
inat <- format_bdvis(inat,source='rinat')
inat <- gettaxo(inat)

Local database taxo.db is absent Processing names not present in local database ... | | 0%No ENTREZ API key provided Get one via taxize::use_entrez() See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/ ══ 1 queries ═══════════════

Retrieving data for taxon 'Acrochordus granulatus'

√ Found: Acrochordus+granulatus ══ Results ═════════════════

Retrieving data for taxon 'Agama'

√ Found: Agama ══ Results ═════════════════

Retrieving data for taxon 'Agamidae'

√ Found: Agamidae ══ Results ═════════════════

Retrieving data for taxon 'Ahaetulla nasuta'

√ Found: Ahaetulla+nasuta ══ Results ═════════════════

This console is showing the same error endlessly.

Session_Info.txt