Tibble error when trying to download Chordate COI database from NCBI

[MarkGillingham]

Hi François,

Thanks for the great code to download NCBI data into R. I have managed to download a large amount of COI NCBI data already for arthoprods and other taxa. Unfortunately I encounter an error when trying to download Chordate COI data.

Below is my code:

chordate_df_refdb<-refdb_import_NCBI("(cytochrome c oxidase subunit 1[Title] OR cytochrome c oxidase subunit I[Title] OR cytochrome oxidase subunit 1[Title] OR cytochrome oxidase subunit I[Title] OR COX1[Title] OR CO1[Title] OR COI[Title] AND mitochondrion[Filter] NOT environmental sample[Title] NOT environmental samples[Title] NOT environmental[Title] NOT uncultured[Title]) NOT unclassified[Title] NOT unidentified[Title] NOT unverified[Title]) AND (Chordata[organism])")

Here is the error message:
`Downloading 420377 sequences from NCBI...

81000 (19.3%) sequences downloaded.
Something went wrong:
HTTP failure: 500
{"error":"error forwarding request","api-key":"2a04:6ec0:20d:c5a0:1cae:305c:821e:6390","type":"ip",
"status":"ok"}
Retrying in 0 s.
Error:
! Tibble columns must have compatible sizes.
• Size 200: Existing data.
• Size 204: Column id.
ℹ Only values of size one are recycled.
`

It seems that for some reason when downloading a specific NCBI entry, it is creating columns of different lengths then the rest of the data. Would you by any chance be able to fix this bug?

Many thanks!!

Mark

[fkeck]

Hi Mark,
I am looking at your issue, but this kind of problem are most likely on the side of NCBI and are hard to investigate.
I will keep you informed of my progress here.
François

[fkeck]

Hi Mark,
I just tested with your command and it worked after the patch 8e7d896
Please use the GitHub version of the package, as no CRAN release is planned soon.
François