[R-sig-Geo] Load spatialite extension in RSQLite crashes R (OS X 10.8)

[Peter Schmiedeskamp]

Thanks Alex,

I'm in the thick of working with this now, and literally just
discovered that libspatialite.so.3 loads in Ubuntu and OS X (however,
queries exercising spatial functions still cause R to segfault on OS
X, but I'll take this as forward progress).

If you don't mind, I'll forward this thread on to the spatialite users
group. I've seen a few postings focussed on other languages that talk
about extension loading problems with the new libspatialite.

Cheers,
Peter


On Sat, Aug 10, 2013 at 11:57 AM, Alex Mandel
<tech_dev at wildintellect.com> wrote:
> That's entirely possible Spatialite 4 had some changes to the db
> structure when compared to Spatialite 3. I don't think RSQLite or
> Pyspatialite have caught up yet, and SQLiteMap (R package) appears
> orphaned. So I would try to roll back to spatialite 3 and see if you can
> get that working with SQLiteMap. That also appears to mean R below
> version 3.
>
> So in Raring (13.04) that means use it from the main ubuntu repos.
> On Mac http://www.kyngchaos.com/software:frameworks  Spatialite Tools v3.0
>
> Possible workaround, create a view and then use rgdal (with gdal 1.10)
> to import that view.
>
> I tested on ubuntu 12.04 and those instructions (which I wrote) don't
> appear to work anymore, at least not with R 3.0+spatialite3. I
> originally figured that out back in 2008-2009 though so a lot has
> changed since then. I'm going to go back to OSGeoLive 6.5 and see if
> they work (that should have R 2.15 with spatialite3)
>
> Thanks,
> Alex
>
> On 08/09/2013 01:57 PM, Peter Schmiedeskamp wrote:
>> I fired up an Ubuntu VM and found that loading the spatialite
>> extension also seems to crash there. My test Ubuntu setup is v13.04
>> (x86_64). I installed libspatialite5 from the Ubuntu FOSS GIS
>> packages: (http://hub.qgis.org/projects/quantum-gis/wiki/Download#262-With-updated-dependencies).
>> R was installed from the CRAN Ubuntu package site.
>>
>> I am starting to wonder if this isn't an incompatibility between
>> RSQLite and the latest versions of libspatialite. If anyone has any
>> experience using the new libspatialite with RSQLite, I'd love to hear
>> how you got it working.
>>
>> Cheers,
>> Peter
>>
>> On Thu, Aug 8, 2013 at 7:08 PM, Peter Schmiedeskamp
>> <peter at thoughtspot.net> wrote:
>>> I am running some queries against a spatialite database, and would
>>> like to get the data directly into R.This thread
>>> (http://r-sig-geo.2731867.n2.nabble.com/Re-spatialite-from-R-td7583603.html)
>>> suggests I can do something like this:
>>>
>>> library(RSQLite)
>>> sqldrv <- dbDriver("SQLite")
>>> con <- dbConnect(sqldrv, dbname =
>>> "/path/to/db.sqlite",loadable.extensions = TRUE)
>>> spatialitestatus <- dbGetQuery(con, "SELECT
>>> load_extension('libspatialite.dylib')")
>>>
>>> But when I do, R segfaults with the following:
>>>
>>>  *** caught segfault ***
>>> address 0x0, cause 'memory not mapped'
>>>
>>> Traceback:
>>>  1: .Call("RS_SQLite_fetch", rsId, nrec = n, PACKAGE = .SQLitePkgName)
>>>  2: sqliteFetch(rs, n = -1, ...)
>>>  3: sqliteQuickSQL(conn, statement, ...)
>>>  4: dbGetQuery(con, "SELECT
>>> load_extension('/usr/local/lib/libspatialite.dylib')")
>>>  5: dbGetQuery(con, "SELECT
>>> load_extension('/usr/local/lib/libspatialite.dylib')")
>>>
>>> In my case, spatialite was built from source using Homebrew, as is the
>>> version of sqlite that I would normally use. In the libspatialite
>>> homebrew definition, it says it depends on sqlite > 3.7.3. My
>>> homebrewed version of sqlite is 3.7.17. My libspatialite is
>>> libspatialite-4.1.1.
>>>
>>> I don't know for certain what version of sqlite RSQLite pulls in by
>>> default, but I assume it's the version 3.7.17 version included in the
>>> RSQLite source package. I tried building RSQLite from source
>>> usinginstall.packages(c("RSQLite"), type="source") in hopes that it
>>> would simply use my version of sqlite, but it doesn't look like it
>>> did. Or if it did, it's still crashing.
>>>
>>> Finally, I should mention that I tried this under two versions of R
>>> with same results:
>>>
>>> R 3.0.0 downloaded in binary form from CRAN
>>> R 3.0.1 downloaded in source form and installed via homebrew
>>>
>>> Cheers,
>>> Peter
>>>
>>> P.S. I also posted this to stackoverflow a couple days ago, if anyone
>>> is hankering for some karma:
>>> http://stackoverflow.com/questions/18107336/load-spatialite-extension-in-rsqlite-crashes-r-os-x
>>
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