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

[Alex Mandel]

Yes, thats a good place to ask, though you may once again be talking to
me. I did find this old thread I had forgot about, which has some more
ideas.
https://stat.ethz.ch/pipermail/r-sig-db/2010q1/000784.html

Thanks,
Alex

On 08/10/2013 12:02 PM, Peter Schmiedeskamp wrote:
> 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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>>