rgdal install fails (following GDAL building from source)

Dear all,

I'm using the (excellent) rgdal package for a while now, but following
the build from source of the last GDAL stable release, I can not
reinstall it.

When I'm asking for install.packages("rgdal"), I got the following error:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
 unable to load shared library '/usr/lib64/R/library/rgdal/libs/rgdal.so':
 libgdal.so.1: cannot open shared object file: No such file or directory

From some internet search, I understand that it is possibly due to a

change in where GDAL has been installed, but I've been unsuccessful to
fix that so far.

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

Does gdalinfo --version run? Did you run ldconfig -v as su after
installing GDAL?

Check that GDAL itself can find its own shared objects,
if it can, then so should rgdal.

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

Thanks for the reply Roger,

Does gdalinfo --version run? Did you run ldconfig -v as su after
installing GDAL?

Yes, I ran su -c 'ldconfig -v' after the make install, and at the
moment gdalinfo --version gives me the good output (GDAL 1.7.2,
released 2010/04/23).

Check that GDAL itself can find its own shared objects,
if it can, then so should rgdal.

How could I do that? I had the same idea that if GDAL is running,
rgdal should be running as well, but I only checked using gdalinfo.

Moreover, if it could be of any help, here is the interesting bit
during the compilation of rgdal:

...
checking for pj_init_plus in -lproj... yes
./proj_conf_test: error while loading shared libraries: libgdal.so.1:
cannot open shared object file: No such file or directory
./proj_conf_test: error while loading shared libraries: libgdal.so.1:
cannot open shared object file: No such file or directory
Package CPP flags: -I/usr/local/include
Package LIBS: -L/usr/local/lib -lgdal
...

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

Is PROJ.4 installed correctly? There is no reason for it to depend on GDAL
- my RHEL5 says:

$ ldd `which proj`
         libproj.so.0 => /usr/local/lib/libproj.so.0 (0x00002adcf57b0000)
         libm.so.6 => /lib64/libm.so.6 (0x000000308bc00000)
         libc.so.6 => /lib64/libc.so.6 (0x000000308b800000)
         /lib64/ld-linux-x86-64.so.2 (0x000000308b400000)

and

$ proj
Rel. 4.7.1, 23 September 2009
usage: proj [ -beEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]

with no dependency on GDAL. Do you maybe have a stale GRASS GDAL plugin
hanging around?

Roger

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

Hi again,

Is PROJ.4 installed correctly? There is no reason for it to depend on GDAL
- my RHEL5 says:

$ ldd `which proj`
         libproj.so.0 => /usr/local/lib/libproj.so.0 (0x00002adcf57b0000)
         libm.so.6 => /lib64/libm.so.6 (0x000000308bc00000)
         libc.so.6 => /lib64/libc.so.6 (0x000000308b800000)
         /lib64/ld-linux-x86-64.so.2 (0x000000308b400000)

and

$ proj
Rel. 4.7.1, 23 September 2009
usage: proj [ -beEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]

It seems to be correctly installed:

xx$ ldd `which proj`
       linux-vdso.so.1 =>  (0x00007fff6ef08000)
       libproj.so.0 => /usr/lib64/libproj.so.0 (0x0000003e29000000)
       libm.so.6 => /lib64/libm.so.6 (0x0000003e26800000)
       libc.so.6 => /lib64/libc.so.6 (0x0000003e26400000)
       /lib64/ld-linux-x86-64.so.2 (0x0000003e26000000)

xx$ proj
Rel. 4.7.1, 23 September 2009
usage: proj [ -beEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]

with no dependency on GDAL. Do you maybe have a stale GRASS GDAL plugin
hanging around?

That is most likely indeed, as I tried (and failed) to build the GRASS
GDAL plugin from source!

What is the exact library that may mess this all up?

Thanks again,

Pierre

Roger

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

I think that there is a GDAL plugins directory somewhere in /usr/local - if
it is there, it contains a reference to your previous GDAL install, probably
called gdalplugins. Try removing it, or changing its name.

Roger

Thanks again,

Pierre

Roger

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School
of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

I think that there is a GDAL plugins directory somewhere in /usr/local - if
it is there, it contains a reference to your previous GDAL install, probably
called gdalplugins. Try removing it, or changing its name.

Yes, there was a gdalplugins folder in /usr/lib/, containing
ogr_GRASS.so. I removed the whole folder, but unfortunatley, the same
error is appearing on compilation of rgdal.

Thanks anyway,

Pierre

Roger

Thanks again,

Pierre

Roger

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School
of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

There must still be messes left around in various places. Does using locate,
for example locate libgdal and locate gdalplugins help? Otherwise remove and
reinstall PROJ.4 and GDAL. Most likely debris after experiments with the
GRASS plugin (and maybe QGIS) are still around.

Roger

Thanks anyway,

Pierre

Roger

Thanks again,

Pierre

Roger

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School
of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School
of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

On Mon, 19 Jul 2010, Pierre Roudier wrote:

I think that there is a GDAL plugins directory somewhere in /usr/local -
if
it is there, it contains a reference to your previous GDAL install,
probably
called gdalplugins. Try removing it, or changing its name.

Yes, there was a gdalplugins folder in /usr/lib/, containing
ogr_GRASS.so. I removed the whole folder, but unfortunatley, the same
error is appearing on compilation of rgdal.

There must still be messes left around in various places. Does using locate,
for example locate libgdal and locate gdalplugins help? Otherwise remove and
reinstall PROJ.4 and GDAL. Most likely debris after experiments with the
GRASS plugin (and maybe QGIS) are still around.

Roger

Thanks anyway,

Pierre

Roger

Thanks again,

Pierre

Roger

Thanks for the help,

Pierre

Hope this helps,

Roger

Thanks for any hints.

Here is my config:

uname -a
Linux 2.6.33.6-147.fc13.x86_64 #1 SMP Tue Jul 6 22:32:17 UTC 2010
x86_64 x86_64 x86_64 GNU/Linux

Distro : Fedora 13 x86_64 (running KDE)

gdalinfo --version
GDAL 1.7.2, released 2010/04/23

The infamous libgdal.so file is located in /usr/local/lib/

sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-redhat-linux-gnu

locale:
[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C
[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

loaded via a namespace (and not attached):
[1] tcltk_2.11.1 tools_2.11.1

Cheers,

Pierre

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School
of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School
of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, 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