Linking problem with rgdal

Hi Rainer,

Thanks for the reply - your memory clearly serves you well,
although I had to add both proj.4 and gdal to the LD_LIBRARY_PATH
to get it to work fully ie.

export
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/R/gdal/lib/:$HOME/R/proj4/lib

 I clearly owe you a beer :-)

I can add this to my .bashrc, so that it is loaded every time I
login but is there any other "more permanent" solution?

Best wishes,

Mark


On 4 February 2014 14:22, Rainer M Krug <Rainer at krugs.de> wrote: On
02/04/14, 13:23 , Mark Payne wrote:

Hi,

I'm trying to install rgdal on a Scientific LInux cluster
which I do not have administrator rights. So far, I have done
the following * Downloaded and installed gdal from source
into my home directory ie configured with ./configure
--prefix=$HOME/R/gdal *Downloaded and install proj4 from
source with a similar configuration ./configure
--prefix=$HOME/R/proj4/

Next, I try to install the rgdal package specifying the
various locations

R CMD INSTALL rgdal_0.8-14.tar.gz 
--configure-args='--with-proj-lib=$HOME/R/proj4/lib 
--with-proj-include=$HOME/R/proj4/include 
--with-gdal-config=$HOME/R/gdal/bin/gdal-config' --preclean 
--no-clean-on-error

This generally works up to the point where it tries to do a
test load, giving the message: .... ** testing if installed
package can be loaded Error in dyn.load(file, DLLpath =
DLLpath, ...) : unable to load shared object 
'/zhome/39/c/38865/R/x86_64-unknown-linux-gnu-library/3.0/rgdal/libs/rgdal.so':

Error: loading failed Execution halted ERROR: loading failed

If I check the contents of the shared object: ldd 
~/R/x86_64-unknown-linux-gnu-library/3.0/rgdal/libs/rgdal.so 
linux-vdso.so.1 =>  (0x00007fff74dff000) libgdal.so.1 => not
found libproj.so.0 => not found libR.so => not found
libstdc++.so.6 => /usr/lib64/libstdc++.so.6
(0x00007f59fe330000) libm.so.6 => /lib64/libm.so.6
(0x00007f59fe0ab000) libgcc_s.so.1 => /lib64/libgcc_s.so.1
(0x00007f59fde95000) libc.so.6 => /lib64/libc.so.6
(0x00007f59fdb01000) /lib64/ld-linux-x86-64.so.2 
(0x00000039b3600000)

So for some reason although the build process is recognising
the libraries, it is not storing their location  in the
shared object.

I stand to be corrected, as I haven't done this for quite some
time:

The paths you specify are for compile time, the ones missing are
for run time. So you have to add the library path of gdal to your
library paths, e.g. via setting the variable LD_LIBRARY_PATH

Hope this helps,

Rainer

This is where my knowledge breaks down. I wonder if I need
to force the build to make static libraries, rather than
dynamically linked ones. But I'm not sure I know what I'm
talking about.

Any suggestions would be appreciated.

Mark