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darwin-eu / DashboardExport

Export descriptive statistics from a subset of Achilles results for the DARWIN EU® Database Dashboard.
Apache License 2.0
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error when code is executed #2

Open kkatsano opened 1 month ago

kkatsano commented 1 month ago

We are trying to run the code on ubuntu server 20.04 and got the following error:

Executing SQL took 0.00408 secs An error report has been created at achilles_output/errorReportR.txt Error in rJava::.jcall(connection@jConnection, "V", "close") : ignoring SIGPIPE signal

DashboardExport::dashboardExport( connectionDetails = connectionDetails, cdmDatabaseSchema = cdmDatabaseSchema, resultsDatabaseSchema = resultsDatabaseSchema, outputFolder = "output", databaseId = databaseId, smallCellCount = 5

We seem to run all the analyses from Analysis 0 to Analysis 2204 and the get the error above. So far we tried different versions of R-namely R.4.4.1, R.4.3.1, R.4.2.3 and also different versions of java: The built-in Java (11.0.24) and the one that we got for linux posted here https://ohdsi.github.io/Hades/rSetup.html

  1. openjdk version "11.0.24" 2024-07-16 OpenJDK Runtime Environment (build 11.0.24+8-post-Ubuntu-1ubuntu320.04) OpenJDK 64-Bit Server VM (build 11.0.24+8-post-Ubuntu-1ubuntu320.04, mixed mode, sharing)
  2. openjdk version "1.8.0_422" OpenJDK Runtime Environment Corretto-8.422.05.1 (build 1.8.0_422-b05) OpenJDK 64-Bit Server VM Corretto-8.422.05.1 (build 25.422-b05, mixed mode)

Would you be able to tell us please what should we do to make it run?

MaximMoinat commented 2 days ago

Did you already solve the issue?

A SIGPIPE signal is often a database connection issue. e.g. the database times out. At what step in the process does this occur (at the beginning, or while running a specific analysis)? And could you share the content of achilles_output/errorReportR.txt?