read.accession not working; preparedatabase failed

[lcamVz]

I've been trying to get the databases to download and get the taxonomy working.

lastly I got this error.

Reading NCBI_DATABASE/nucl_gb.accession2taxid.gz.
Error in readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) :
error reading from the connection
In addition: Warning message:
In readBin(inn, what = raw(0L), size = 1L, n = BFR.SIZE) :
invalid or incomplete compressed data

packageVersion('taxonomizr')
[1] ‘0.6.0’

[sherrillmix]

A bit more output might be useful for debugging but that sounds like it may be a download problem. Could you redownload NCBI_DATABASE/nucl_gb.accession2taxid.gz and/or check to see that its filesize is close to the expected 8263483 KB or that its md5 matches:
ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/nucl_gb.accession2taxid.gz.md5

[lcamVz]

Thank you for the quick reply.

I manually download them from the ftp and it worked I used wget -i list.txt to get all of the nucleic and protein.

[sherrillmix]

That's good it ended up working for you. The package has had a few hard to replicate reports of download problems lately e.g. #27. Not sure what's causing them but I think when I get a chance I'll add an automatic md5 check after the download to at least catch when they happen. Thanks for the bug report.