[R-sig-Debian] Querying sqlite through RODBC causes R to crash

[Tom Gottfried]

Here comes what is almost self-contained. Unfortunately I was not able 
to find a command-line tool to configure the ODBC DSN.


apt-get install r-cran-rodbc libsqliteodbc sqlite3 unixodbc-bin \
	r-cran-rsqlite

sqlite3 testdb.sqlite 'create table test
	(id integer primary key, test text);
	insert into test values (1, "test");'

ODBCManageDataSourcesQ4
# add DSN with name 'testdb' referring to
# testdb.sqlite with SQLite3 driver

echo 'library(RODBC)
	sqlQuery(odbcConnect("testdb"), "select * from test")' |
	R --vanilla
	# crashes R

echo 'library(RSQLite)
	dbGetQuery(dbConnect("SQLite", dbname="testdb.sqlite"),
	"select * from test")' |
	R --vanilla
	# returns a data.frame as expected

Am 27.08.2012 15:12, schrieb Dirk Eddelbuettel:
>
> 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
> |
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>

-- 
Indo-German Centre for Sustainability
Indian Institute of Technology Madras
600 036 Chennai, India
www.igcs-chennai.org