R SIG Debian - Aug 2011 - rgdal cannot load shared object

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:

---<--------------------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.

Is this a transient problem in sid or something else?  Thanks.


Cheers,

-- 
Seb

On Wed, 24 Aug 2011 13:30:37 +0200,
Roger Bivand <Roger.Bivand at nhh.no> wrote:
> 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.
Thanks Roger; I tried reinstalling rgdal, and got some more clues
following install.packages("rgdal") (relevant lines only):

/usr/lib/libgdal1.7.0.so: undefined reference to
`libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
./configure: line 3366: ./proj_conf_test: No such file or directory
PROJ.4 Version 4.7 or earlier
/usr/lib/libgdal1.7.0.so: undefined reference to
`libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
./configure: line 3409: ./proj_conf_test: No such file or directory
/usr/lib/libgdal1.7.0.so: undefined reference to
`libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
./configure: line 3459: ./proj_conf_test: No such file or directory

and:

/usr/lib/libgdal1.7.0.so: undefined reference to
`libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
./configure: line 3366: ./proj_conf_test: No such file or directory
PROJ.4 Version 4.7 or earlier
/usr/lib/libgdal1.7.0.so: undefined reference to
`libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
./configure: line 3409: ./proj_conf_test: No such file or directory
/usr/lib/libgdal1.7.0.so: undefined reference to
`libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
collect2: ld returned 1 exit status
./configure: line 3459: ./proj_conf_test: No such file or directory

in addition to the error I previously reported.  So AFAICS, it seems
like a problem with Debian sid's libgdal1-1.7.0 or one of the libdap
packages, given the "undefined reference to
'libdap::AISConnect::AISConnect(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
line.

Cheers,

-- 
Seb