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Achilles error generating tables

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#1

Hi everyone,

We are trying to to execute Achilles, and we are having this error:

Connecting using Oracle driver

  • using THIN to connect

CDM Version 5.4 found in cdm_source table.

CDM Version 5.4 found in cdm_source table.

Connecting using Oracle driver

  • using THIN to connect

Beginning multi-threaded execution

Beginning multi-threaded execution

Connecting using Oracle driver

  • using THIN to connect

    |==============================================================================================================| 100%

Executing SQL took 0.129 secs

Inserting data took 0.249 secs

Dropping scratch Achilles tables from schema OMOP_ACHILLES

Dropping scratch Achilles tables from schema OMOP_ACHILLES

|==============================================================================================================| 100%

Temporary Achilles tables removed from schema OMOP_ACHILLES

Temporary Achilles tables removed from schema OMOP_ACHILLES

Executing multiple queries. This could take a while

Executing multiple queries. This could take a while

|==============================================================================================================| 100%

Merging scratch Achilles tables

Merging scratch Achilles tables

| | 0%Thread 1 returns error: “Error executing SQL:njava.sql.SQLSyntaxErrorException: ORA-00942: table or view does not existnnAn error report has been created at C:/Users/ladm.allorente/Documents/errorReportSql.txt” when using argument(s): x = " BEGINn EXECUTE IMMEDIATE ‘TRUNCATE TABLE OMOP_ACHILLES.achilles_results’;n EXECUTE IMMEDIATE ‘DROP TABLE OMOP_ACHILLES.achilles_results’;nEXCEPTIONn WHEN OTHERS THENn IF SQLCODE != -942 THENn RAISE;n END IF;nEND;n–HINT DISTRI…

Thread 1 returns error: “Error executing SQL:njava.sql.SQLSyntaxErrorException: ORA-00942: table or view does not existnnAn error report has been created at C:/Users/ladm.allorente/Documents/errorReportSql.txt” when using argument(s): x = " BEGINn EXECUTE IMMEDIATE ‘TRUNCATE TABLE OMOP_ACHILLES.achilles_results’;n EXECUTE IMMEDIATE ‘DROP TABLE OMOP_ACHILLES.achilles_results’;nEXCEPTIONn WHEN OTHERS THENn IF SQLCODE != -942 THENn RAISE;n END IF;nEND;n–HINT DISTRI…

|======================================================= | 50%Thread 2 returns error: “Error executing SQL:njava.sql.SQLSyntaxErrorException: ORA-00942: table or view does not existnnAn error report has been created at C:/Users/ladm.allorente/Documents/errorReportSql.txt” when using argument(s): x = " BEGINn EXECUTE IMMEDIATE ‘TRUNCATE TABLE OMOP_ACHILLES.achilles_results_dist’;n EXECUTE IMMEDIATE ‘DROP TABLE OMOP_ACHILLES.achilles_results_dist’;nEXCEPTIONn WHEN OTHERS THENn IF SQLCODE != -942 THENn RAISE;n END IF;nEND;n–H…

Thread 2 returns error: “Error executing SQL:njava.sql.SQLSyntaxErrorException: ORA-00942: table or view does not existnnAn error report has been created at C:/Users/ladm.allorente/Documents/errorReportSql.txt” when using argument(s): x = " BEGINn EXECUTE IMMEDIATE ‘TRUNCATE TABLE OMOP_ACHILLES.achilles_results_dist’;n EXECUTE IMMEDIATE ‘DROP TABLE OMOP_ACHILLES.achilles_results_dist’;nEXCEPTIONn WHEN OTHERS THENn IF SQLCODE != -942 THENn RAISE;n END IF;nEND;n–H…

|==============================================================================================================| 100%

Merging scratch Achilles tables (merging scratch Achilles tables) [ERROR] (Error in ParallelLogger::clusterApply(cluster = cluster, x = mergeSqls, : Error(s) when calling function ‘fun’, see earlier messages for details

)

Merging scratch Achilles tables (merging scratch Achilles tables) [ERROR] (Error in ParallelLogger::clusterApply(cluster = cluster, x = mergeSqls, : Error(s) when calling function ‘fun’, see earlier messages for details

)

Done. Achilles results can now be found in schema OMOP_ACHILLES

Done. Achilles results can now be found in schema OMOP_ACHILLES

Dropping scratch Achilles tables from schema OMOP_ACHILLES

Dropping scratch Achilles tables from schema OMOP_ACHILLES

|==============================================================================================================| 100%

Temporary Achilles tables removed from schema OMOP_ACHILLES

Temporary Achilles tables removed from schema OMOP_ACHILLES

Connecting using Oracle driver

  • using THIN to connect

    | | 0%An error report has been created at H:/OMOP QC/CDM Inspector/ACHILLES/errorReportR.txt

Error in .createErrorReport():

! Error executing SQL:

java.sql.SQLSyntaxErrorException: ORA-00942: table or view does not exist

An error report has been created at C:/Users/ladm.allorente/Documents/errorReportSql.txt

Run rlang::last_trace() to see where the error occurred.

Warning message:

In as.POSIXlt.POSIXct(x, tz) : unable to identify current timezone ‘C’:

please set environment variable ‘TZ’

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.connectionObserver.errorsSuppressed = TRUE).

Please, could some give us some recomendation to fix it?

thank you!

#2

I was able to resolve this error by going back to Achilles 1.7.0. I’m not sure about the other errors though. I would try that first, though. The command I used was this remotes::install_github("OHDSI/Achilles@v1.7.0")

#3

Hi @Minerva_Alvarez - We have been seeing the same issue Getting an error running achilles.

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