R SIG Debian - Aug 2012 - Querying sqlite through RODBC causes R to crash

Dear R-SIG-Debian,

while trying to query data from an SQLite database through RODBC on 
Debian testing, R crashes with the following message:

library(RODBC)
con3 <- odbcConnect("test3")
# 'test3' being an ODBC datasource configured with SQLite3 driver,
# but the same happens with SQLite driver
sqlQuery(con3, "select * from test") # 'test' being any table

  *** caught segfault ***
address 0x438, cause 'memory not mapped'

Traceback:
  1: .Call(C_RODBCQuery, attr(channel, "handle_ptr"), 
as.character(query),     as.integer(rows_at_time))
  2: odbcQuery(channel, query, rows_at_time)
  3: sqlQuery(con3, "select * from test")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
aborting ...
Segmentation fault



This is what sessionInfo says:

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RODBC_1.3-6



I tested the same under Windows 7 with the same sqlite-file without any 
problem. sessionInfo for the Windows-system:

R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RODBC_1.3-6

loaded via a namespace (and not attached):
[1] tools_2.15.1



On the Debian system, both R and RODBC were installed from the Debian 
repositories. I also tried with an RODBC build from source with the R 
mechanisms (install.packages()), which results in the same error.

Any idea what is the cause or how I could sort it out?

Thank you very much!
Tom
-- 
Indo-German Centre for Sustainability
Indian Institute of Technology Madras
600 036 Chennai, India
www.igcs-chennai.org

On 27 August 2012 at 11:46, Tom Gottfried wrote:
| Dear R-SIG-Debian,
| 
| while trying to query data from an SQLite database through RODBC on 
| Debian testing, R crashes with the following message:
| 
| library(RODBC)
| con3 <- odbcConnect("test3")
| # 'test3' being an ODBC datasource configured with SQLite3 driver,
| # but the same happens with SQLite driver
| sqlQuery(con3, "select * from test") # 'test' being any
table

Please provide a self-contained example which 

  -- creates a tempfile
  -- puts a sqlite3 db into it
  -- access this temp db from R
  -- has R crashing

as there is nothing reproducible in your report.  I would also suggest to
skip ODBC at first and focus on the RSQLite package.

Dirk

| 
|   *** caught segfault ***
| address 0x438, cause 'memory not mapped'
| 
| Traceback:
|   1: .Call(C_RODBCQuery, attr(channel, "handle_ptr"), 
| as.character(query),     as.integer(rows_at_time))
|   2: odbcQuery(channel, query, rows_at_time)
|   3: sqlQuery(con3, "select * from test")
| 
| Possible actions:
| 1: abort (with core dump, if enabled)
| 2: normal R exit
| 3: exit R without saving workspace
| 4: exit R saving workspace
| Selection: 1
| aborting ...
| Segmentation fault
| 
| 
| 
| This is what sessionInfo says:
| 
| R version 2.15.1 (2012-06-22)
| Platform: x86_64-pc-linux-gnu (64-bit)
| 
| locale:
| [1] C
| 
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base
| 
| other attached packages:
| [1] RODBC_1.3-6
| 
| 
| 
| I tested the same under Windows 7 with the same sqlite-file without any 
| problem. sessionInfo for the Windows-system:
| 
| R version 2.15.1 (2012-06-22)
| Platform: x86_64-pc-mingw32/x64 (64-bit)
| 
| locale:
| [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
| [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
| [5] LC_TIME=German_Germany.1252
| 
| attached base packages:
| [1] stats     graphics  grDevices utils     datasets  methods   base
| 
| other attached packages:
| [1] RODBC_1.3-6
| 
| loaded via a namespace (and not attached):
| [1] tools_2.15.1
| 
| 
| 
| On the Debian system, both R and RODBC were installed from the Debian 
| repositories. I also tried with an RODBC build from source with the R 
| mechanisms (install.packages()), which results in the same error.
| 
| Any idea what is the cause or how I could sort it out?
| 
| Thank you very much!
| Tom
| -- 
| Indo-German Centre for Sustainability
| Indian Institute of Technology Madras
| 600 036 Chennai, India
| www.igcs-chennai.org
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com