Comments (1)
Hmm. It seems to be working here:
> taxonomizr::prepareDatabase('accessionTaxa.sql')
Downloading names and nodes with getNamesAndNodes()
trying URL 'ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz'
Content type 'unknown' length 54055484 bytes (51.6 MB)
==================================================
...
NCBI seems to have occasional networking difficulties. I know you already double checked with wget but could you repeat the R command again to check if there was some sort of blip?
Failing that could you post the results of sessionInfo()
to start narrowing down what could be causing an issue.
from taxonomizr.
Related Issues (20)
- FR: set a variable with default path for the databases HOT 5
- read.names.sql for common names HOT 2
- Assignment of taxonomy to blast hits HOT 1
- error: no such column: tmp.query.accession HOT 1
- Manual preparation of database HOT 1
- Error in preparing accessionTaxa.sql with prepareDatabase() HOT 10
- Get all bacterial species HOT 2
- Questions for the issue of taxonomizr package being terminated during operation HOT 1
- Error: disk I/O error In addition: Warning message: Couldn't set synchronous mode: disk I/O error HOT 5
- accessionToTaxa returns a single NA when the input contains too many accession ID HOT 3
- Error in downloading database using prepareDatabase HOT 9
- prepareDatabase('accessionTaxa.sql') downloading names and nodes with getnamesandnodes() error: HOT 9
- Error:database is locked with prepareDatabase HOT 3
- Cannot get taxonomizr to work HOT 4
- Pointing R to an already prepared database HOT 4
- Unable to query SQL database when built with `getAccessions=FALSE` HOT 2
- Does this tool do LCA? HOT 1
- Exclude species with no rank HOT 1
- error in prepareDatabase HOT 3
- Error in prepareDatabase('accessionTaxa.sql'), change in url? HOT 3
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from taxonomizr.