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Warning while running Achilles


(Gigi Lipori) #1

When I run achilles and heel, using the code below, I get the error: “The schema argument is deprecated. Please use fully specified table names in your SQL statement, for example 'SELECT * FROM my_schema.my_table;” Is this problematic? Is there an appropriate workaround? The code runs to completion and the subset of reports that render in Atlas without error contain plausible results. Appreciate any thoughts.

run latest Achilles

library(Achilles)
setwd("~/Desktop/ohdsi/test")

start_time <- Sys.time()

connect to postgres database containing CDMs

connectionDetails <- createConnectionDetails(dbms=“postgresql”,
server=“127.0.0.1/omop”,
user=“postgres”,
password=‘xxxxx’,
schema=“test”, port=“5432”)

run achilles (and achilles heel) in a single thread

achillesResults <- achilles(connectionDetails, cdmDatabaseSchema=“test”,
resultsDatabaseSchema=“test_results”, sourceName=“test”,
cdmVersion = “5.3”, vocabDatabaseSchema=“test”,
runCostAnalysis = FALSE, runHeel = TRUE, smallCellCount = 0,
scratchDatabaseSchema = “test_results”,
numThreads = 5)

end_time <- Sys.time()
writeLines(paste("start - ",start_time, " end - ", end_time))


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