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ropensci / taxizedb

Tools for Working with Taxonomic SQL Databases
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Could not resolve host: ftp.ncbi.nih.gov #74

Closed mkhemmani closed 3 months ago

mkhemmani commented 5 months ago

Hello, I'm having an issue running the taxizedb::name2taxid function on ncbi database taxaonomy

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library(taxizedb)
db_download_ncbi()

Error in curl::curl_download(db_url, db_path_file, quiet = TRUE) : Could not resolve host: ftp.ncbi.nih.gov

taxizedb::name2taxid("Corynebacterium", db="ncbi", out_type = "summary")

Error in curl::curl_download(db_url, db_path_file, quiet = TRUE) : Could not resolve host: ftp.ncbi.nih.gov

Should the ncbi database url be db_url<-"https://ftp.ncbi.nlm.nih.gov/" ? https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

NOT ftp.ncbi.nih.gov?

KaiAragaki commented 5 months ago

@mkhemmani As best as I can tell, you are correct: the endpoint has updated. I made a PR (#73) that should fix this, which you can use in the meantime if you'd like.

KaiAragaki commented 4 months ago

@mkhemmani This issue appears to have resolved itself - maybe NCBI updated their redirects? unclear.

mkhemmani commented 4 months ago

Looks like both addresses are valid, now.