Databases
StackOverflow2013
Postsdbo
POLoad spatialite extension in RSQLite crashes R (OS X & Ubuntu)
 

Note that there are some explanatory texts on larger screens.

plurals
  1. POLoad spatialite extension in RSQLite crashes R (OS X & Ubuntu)
    primarykey
    data
    text
    <p>I am running some queries against a spatialite database, and would like to get the data directly into R. <a href="http://r-sig-geo.2731867.n2.nabble.com/Re-spatialite-from-R-td7583603.html" rel="nofollow">This page</a> suggests I can do something like this:</p> <pre><code>library(RSQLite) sqldrv &lt;- dbDriver("SQLite") con &lt;- dbConnect(sqldrv, dbname = "/path/to/db.sqlite",loadable.extensions = TRUE) spatialitestatus &lt;- dbGetQuery(con, "SELECT load_extension('libspatialite.dylib')") </code></pre> <p>But when I do, R segfaults with the following:</p> <pre><code> *** 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')") </code></pre> <p>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</p> <p>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 using <code>install.packages(c("RSQLite"), type="source")</code> 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.</p> <p>Finally, I should mention that I tried this under two versions of R with same results:</p> <ul> <li>R 3.0.0 downloaded in binary form from CRAN</li> <li>R 3.0.1 downloaded in source form and installed via homebrew</li> </ul> <h2>UPDATE:</h2> <p>Crash confirmed in Ubuntu 13.04 using the libspatialite5 provided by the Ubuntu FOSS GIS repository.</p>
    singulars
    1. PO
      singulars
      1. PTAnswer
    1. This table or related slice is empty.
    1. PTQuestion
    1. USPeter
    1. USPeter
    plurals
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. PO
      singulars
      1. PTAnswer
    1. This table or related slice is empty.
    1. COThe maintainer of the Mac branch, Simon Urbanek, recommends not using any of MacPorts, Homebrew or Fink for installation of external packages.
      singulars
      1. POLoad spatialite extension in RSQLite crashes R (OS X & Ubuntu)
      1. US42-
    2. COWhat do you mean by external packages? Non-R system libraries? In the case of spatialite, I have no idea where I'd even download a pre-built binary. And if I were building from source, I'd do exactly what homebrew does.
      singulars
      1. POLoad spatialite extension in RSQLite crashes R (OS X & Ubuntu)
      1. USPeter
    3. COYes, if you prefer non-R system libraries. http://markmail.org/message/cgehvnldhjtaxnwk?q=list:org%2Er-project+urbanek+homebrew+macports As I understand it, problems arise because sources get built into the "wrong" directories. You may get more knowledgeable advice by posting to the Mac-R mailing list.
      singulars
      1. POLoad spatialite extension in RSQLite crashes R (OS X & Ubuntu)
      1. US42-
 

Querying!

 
Guidance
A row detail

Detail views are divided into sections. All the information in the data section comes from columns in the selected row. The other sections display data from other, related rows.

Related data can be related in a to-one or a to-many fashion. Captions of data related in a to-many fashion link to a list view showing a filtered view of the table.

Try moving around until you find a non-empty to-many entry and click on the label to get to one. You can move back to the root by clicking on the database name in the header.

SQuiL has stopped working due to an internal error.

If you are curious you may find further information in the browser console, which is accessible through the devtools (F12).

Reload