[R] Creating a .txt file from an Oracle DB without creating an R object
Marc Schwartz (via MN)
mschwartz at mn.rr.com
Wed Apr 19 18:31:04 CEST 2006
On Wed, 2006-04-19 at 17:14 +0100, Prof Brian Ripley wrote:
> On Wed, 19 Apr 2006, Marc Schwartz (via MN) wrote:
> > On Wed, 2006-04-19 at 17:02 +0200, Paul wrote:
> >> Dear R-helpers,
> >> I am dealing with an Oracle database (using package RODBC). I use
> >> R in order to transform some Oracle tables into .txt files (using
> >> function sqlFetch from package RODBC and then function write.table).
> >> However, I cannot do it without creating an R object, which is rather
> >> restrictive for very big Oracle tables. Indeed, any R Object is stored
> >> into RAM, which can be of limited size.
> >> Do you know if it is possible to directly create a .txt file,
> >> without creating an R object ?
> >> Thank you in advance.
> >> P. Poncet
> > Somebody else may have a better idea, but you could probably use either
> > sink() or capture.output() to send the data to a text file instead of
> > the console, thus not creating an R object. For example:
> > capture.output(sqlFetch(channel, "YourTableName", colnames = TRUE),
> > "OutputFile.txt")
> > You will need to adjust options("width"), which defaults to 80 and would
> > cause the typical in-console line wrapping to occur. You would not want
> > this in your text file of course. 'width' can be set up to 10,000 by
> > default and could go higher, if you want to adjust the value in print.h
> > and re-compile R.
> I don't think this helps: sqlFetch will create an (unnamed) R object
> containing the whole table and hence have the memory issues. What you can
> do is use is a limit on the number of rows and use sqlFetchMore in a loop.
Ah...yes indeed. Now that I looked at the function code, it does create
an internal data frame called 'ans', which is the result of using:
ans <- sqlQuery(channel, paste("SELECT * FROM", dbname),
Looking at the internal code for sqlQuery(), which in turn leads one to
lower level RODBC functions, there is not a "row by row" query result
being returned. The query results in each case appear to be fully stored
in an internal R object first before being returned to the caller.
Thus, Prof. Ripley's loop approach (or one of the myriad external
mechanisms) would be the way to go.
Thanks for the clarification.
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