rgdal cannot load shared object - R-SIG-Debian

Mon, Aug 22, 2011 7:46 AM #

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

Sébastien Bihorel

Wed, Aug 24, 2011 8:40 AM #

On Wed, 24 Aug 2011 13:30:37 +0200,

Roger Bivand <Roger.Bivand at nhh.no> wrote:

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

Rainer M Krug

Thu, Aug 25, 2011 2:15 AM #

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Sébastien Bihorel

Thu, Aug 25, 2011 7:20 AM #

On Thu, 25 Aug 2011 11:15:35 +0200,

Rainer M Krug <r.m.krug at gmail.com> wrote:

On Wed, Aug 24, 2011 at 5:40 PM, Sebastian P. Luque <spluque at gmail.com>wrote:

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.

In my experience, proj usually points to something related to proj4 -
are you sure that proj4 os properly installed, including dev files
(not sure if needed, but likely)?

I think the problem comes from this bug:

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=638294

because when I found this conflict, I went ahead and used "dpkg -i
--force-overwrite ..", which may have botched my libdap.  It looks like
we will soon have a new version.

Cheers,

Seb