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Below is a snippet of my code that I use in R to extract IDs from a PostgreSQL database. When I run the function I get the following warning message from R:

In result_create(conn@ptr, statement) : Closing open result set, cancelling previous query

How do I avoid this warning message from happening without making use of options(warn=-1) at the beginning of my code, suppressing the warning instead of 

con <- dbConnect(RPostgres::Postgres(),
                 user = "postgres",
                 dbname  = "DataBaseName",
                 password  = "123456",
                 port  = 5431)


get_id <- function(connection, table){

  query <- toString(paste("SELECT id FROM ", table, sep = ""))
  data_extract_query <- dbSendQuery(connection, query)
  data_extract <- dbFetch(data_extract_query)
  return(data_extract)
}


get_id(con, "users")
Phil
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cnburger
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2 Answers2

2

I found a method for solving the problem.

I found a thread on GitHub for RSQLite a https://github.com/r-dbi/RSQLite/issues/143. In this thread, they explicitly set n = -1 in the dbFetch() function.

This seemed to solve my problem, and the warning message did not show up again by editing the code like the following:

data_extract <- dbFetch(data_extract_query, n = -1)

The meaning of n is the number of rows that the query should return. By setting this to -1 all rows will be retrieved. By default, it is set to n = -1 but for some reason, in this build of R (3.6.3) the warning will still be shown.

Calling ?dbFetch in R you can see more information on this. I have included a snippet from the R-help page:

Usage

dbFetch(res, n = -1, ...)

fetch(res, n = -1, ...)

Arguments

res An object inheriting from DBIResult, created by dbSendQuery().

n maximum number of records to retrieve per fetch. Use n = -1 or n = Inf to retrieve all pending records. Some implementations may recognize other special values.

... Other arguments passed on to methods.

cnburger
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2

This issue comes up with other database implementations if the results are not cleared before submitting a new one. From the docs of DBI::dbSendQuery

Usage dbSendQuery(conn, statement, ...)

...

Value

dbSendQuery() returns an S4 object that inherits from DBIResult. The result set can be used with dbFetch() to extract records. Once you have finished using a result, make sure to clear it with dbClearResult(). An error is raised when issuing a query over a closed or invalid connection, or if the query is not a non-NA string. An error is also raised if the syntax of the query is invalid and all query parameters are given (by passing the params argument) or the immediate argument is set to TRUE.

To get rid of the warning the get_id() function must be modified as follows:

get_id <- function(connection, table){

  query <- toString(paste("SELECT id FROM ", table, sep = ""))
  data_extract_query <- dbSendQuery(connection, query)
  data_extract <- dbFetch(data_extract_query)

  # Here we clear whatever remains on the server
  dbClearResult(data_extract_query)

  return(data_extract)
}

See Examples section in help for more.

Viktor Horváth
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