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Error in result_create(conn@ptr, statement) : no such table: ... #13

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rerickson-usgs opened this issue Apr 24, 2019 · 2 comments

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commented Apr 24, 2019

I am trying to run code that worked on a co-workers machine.

When I try to run

 taxa <- accessionToTaxa(arthropoda[ condor_index, 1], sqlFile= "accessionTaxa.sql")

I get the following error message

Error in result_create(conn@ptr, statement) :
no such table: accessionTaxa
Timing stopped at: 0.031 0.003 0.036

A quick Google search found this question on SO and a comment one of the answers notes

The problem is that RSQLite 2.0 was just released and does not work with older versions of sqldf. sqldf 0.4-11 which was just released should be used (or else use an older version of RSQLite)

I have tried upgrading taxonomizr and am using taxonomizr_0.5.3. Do you have any suggestions? Or has anyone else seen this with the package before?

@sherrillmix

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commented Apr 24, 2019

That could be something complex but I wonder if something went wrong when making the database. Could you try deleting accessionTaxa.sql and reinstalling with prepareDatabase('accessionTaxa.sql') (note that'll download some big files and take a while to process)?

@rerickson-usgs

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commented Apr 25, 2019

Thank you for the tip. There is some problem with how my machine was regenerating the sql database. (My solution was to just use the sql database generated on my co-workers machine).

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