[R-sig-Geo] rgdal cannot load shared object

[Roger Bivand]

On Tue, 23 Aug 2011, Sebastian P. Luque wrote:

> Hello,
>
> I'm on a Debian sid system, and after a an upgrade of packages ('apt-get
> upgrade') over the weekend, loading rgdal no longer works:

Debian GIS packages are not reliable. The CRAN debian checks failed in 
mid-May with a libgdal upgrade, which got resolved after some time without 
clear diagnoses - possibly an upstream dependency issue in something one 
libgdal build depended on and another not. General advice with Debian and 
derivative systems is to install GDAL from source if possible to avoid 
this kind of issue. The feel of the error message is that some components 
have been built with different C++ versions, so your question about 
re-installing rgdal for upgraded GDAL binaries has two answers, no if C++ 
and its libraries have not changed, yes if they have.

I haven't seen a reply on R-sig-debian, so please report back there too if 
you make progress.

Hope this helps,

Roger

>
> ---<--------------------cut here---------------start------------------->---
> R> library(rgdal)
> Loading required package: sp
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/usr/local/lib/R/site-library/rgdal/libs/rgdal.so':
>  /usr/lib/libgdal1.7.0.so.1: undefined symbol: _ZN6libdap10AISConnectC1ERKSs
> Error: package/namespace load failed for 'rgdal'
> R> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C               LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8     LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
> [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] sp_0.9-84           slmisc_0.8.9        latticeExtra_0.6-18 RColorBrewer_1.0-5  lattice_0.19-31
>
> loaded via a namespace (and not attached):
> [1] grid_2.13.1
> ---<--------------------cut here---------------end--------------------->---
>
> For libgdal libraries the system has:
>
> ---<--------------------cut here---------------start------------------->---
> $ apt-show-versions -r -p 'libgdal.+'
> libgdal-doc/sid uptodate 1.7.3-5
> libgdal1-1.6.0/squeeze uptodate 1.6.3-4+b1
> libgdal1-1.7.0/sid uptodate 1.7.3-5
> libgdal1-dev/sid uptodate 1.7.3-5
> ---<--------------------cut here---------------end--------------------->---
>
> I could remove the 1.6.0 version, but some packages still require it.
>
> Does rgdal need to be updated due to new gdal libraries, or is this a
> Debian-specific problem?  I posted to the R Debian list yesterday, so
> apologies if you read this twice.
>
> Cheers,
>
>

-- 
Roger Bivand
Department of Economics, NHH Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no