On 4 June 2009 at 16:17, Dylan Beaudette wrote:
| Hi,
|
| I recently upgraded to R 2.9.0 on linux x86. After doing so, I switched to
the
| RPostgreSQL package for interfacing with a postgresql database. I am using
| postgresql 8.3.7.
|
| A query that works from the postgresql terminal is causing a segfault when
| executed from R.
|
| My sessionInfo, the error message, and the R code used to generate the error
| are listed below.
|
| I have noticed that a trivial query (SELECT 1 as value) or other queries seem
| to work fine. It is only when I enable the LEFT JOIN (see below) that I get a
| segfault. Could this be related to the treatment of null values?
As per some recent messages on the r-sig-db list, I think that the error is
due to a bug in the handling of 'schema.table' queries. If you just use
'select ... from table' you're fine.
Not sure if this helps you -- someone has to go in and fix the bug.
Dirk
|
| Any ideas?
| Thanks!
| Dylan
|
| Here is the code that caused the error
|
----------------------------------------------------------------------------------------------------
| # libs
| library(RPostgreSQL)
|
| ## query DB
| q <- "
| SELECT deb_lab_data.*
| -- matrix_wet_color_hue as hue, matrix_wet_color_value as value,
| matrix_wet_color_chroma as chroma
| FROM deb_lab_data
| -- LEFT JOIN horizon USING (pedon_id, hz_number)
| WHERE deb_lab_data.pedon_id ~~ '%SJER%'
| ORDER BY deb_lab_data.pedon_id, deb_lab_data.top ASC "
|
| # create an PostgreSQL instance and create one connection.
| drv <- dbDriver("PostgreSQL")
| conn <- dbConnect(drv, host="localhost", dbname="XXX", user="XXX")
| query <- dbSendQuery(conn, q)
| x <- fetch(query, n = -1) # extract all rows
|
----------------------------------------------------------------------------------------------------
|
| Here is the error message in R:
|
----------------------------------------------------------------------------------------------------
| row number 0 is out of range 0..-1
|
| *** caught segfault ***
| address (nil), cause 'memory not mapped'
|
| Traceback:
| 1: .Call("RS_PostgreSQL_exec", conId, statement, PACKAGE
| = .PostgreSQLPkgName)
| 2: postgresqlExecStatement(conn, statement, ...)
| 3: is(object, Cl)
| 4: is(object, Cl)
|
| 5: .valueClassTest(standardGeneric("dbSendQuery"), "DBIResult",
"dbSendQuery")
| 6: dbSendQuery(conn, q)
|
----------------------------------------------------------------------------------------------------
|
|
|
| Here are the details on my R install:
|
----------------------------------------------------------------------------------------------------
| R version 2.9.0 (2009-04-17)
| i686-pc-linux-gnu
|
| locale:
|
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| other attached packages:
| [1] RPostgreSQL_0.1-4 DBI_0.2-4
|
----------------------------------------------------------------------------------------------------
|
|
|
| --
| Dylan Beaudette
| Soil Resource Laboratory
| http://casoilresource.lawr.ucdavis.edu/
| University of California at Davis
| 530.754.7341
|
| ______________________________________________
| R-help@r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
| and provide commented, minimal, self-contained, reproducible code.
--
Three out of two people have difficulties with fractions.
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
