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Getting an error running achilles

Implementers
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#21

I also did this, and I did not see the error message either.

#23

Hi Siyan - Were you able to resolve this issue? Sorry to resurrect an old topic. Could you provide some details how you did if it is resolved?

Specifically regarding this error:
‘Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 62 did not have 6 elements’

#24

Hi @Zachary-Higgins , I have the same issue at the end of the Achilles execution. Had yo resolved it?

Thanks in advance.

#25

Dear all, please I have read the suggestions above and tried them but still getting errors.

My initial error was An error occurred while the ‘DatabaseConnector’ package was updating the RStudio Connections pane: Error in NULL: host must be a single element of type ‘character’ If necessary, these warnings can be squelched by setting options(rstudio.connection Observer.errors Suppressed = TRUE) An error occurred while the ‘DatabaseConnector’ package was updating the RStudio Connections pane: Error in NULL: host must be a single element of type ‘character’ If necessary, these warnings can be squelched by setting options(rstudio.connection Observer.errors Suppressed = TRUE). So I rolled back to Achilles version 1.7.0, and I am getting this error

Connecting using PostgreSQL driver
| | 0%An error report has been created at output/errorReportR.txt
Error in .createErrorReport():
! Error executing SQL:
org.postgresql.util.PSQLException: ERROR: relation “public_public.achilles_results” does not exist
An error report has been created at /Users/kluivert/PhD/Year 1/Sem 2/OMOP CDM/BCBIDemoResults/BCBIDemo/errorReportSql.txt
Run rlang::last_trace() to see where the error occurred.

The code I am using is

options(connectionObserver = NULL)

Running the achilles

library(Achilles)
achilles(connectionDetails = connectionDetails,
cdmDatabaseSchema = “public_public”,
cdmVersion = “5.3”,
resultsDatabaseSchema = “public”,
smallCellCount = 0,
outputFolder = “output”)

I have also tested the database connection and got this

image
image830×115 16.2 KB

I would gladly appreciate any help from the community.

#26

I was able to solve this problem by following this post ERROR: relation "results.achilles_results" does not exist - #4 by liyang

I also realised that running DataQualityDashboard before Achilles helps a lot because DQD gives a more detailed error report than Achilles. Use the error logs to correct mistakes made when transforming the source data to the OMOP CDM.

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