Linking problem with rgdal
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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':
libgdal.so.1: cannot open shared object file: No such file or directory
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
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- -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: Rainer at krugs.de Skype: RMkrug -----BEGIN PGP SIGNATURE----- Version: GnuPG/MacGPG2 v2.0.22 (Darwin) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQEcBAEBAgAGBQJS8OmAAAoJENvXNx4PUvmC/MkH/Am6KkAqbyTf6FukxDrVGKft 3wyHA/Rnb/ujlkVt4/+okjIadE0N9FnKHCFshudDEqvZl2CJdvKedmAE5cERhFS7 actXf8iJKiFklRYlAXIscJ2A7AyKUqIL5NjvDXwiRNLThOvPQ5b4iuv4e9AP18A5 NAfY/zz7pOA2Q2aBvZFFxEX6YC3sLDo2cf8hxZoBpqaTeUpvZ5k0i0ND1FGE82mE T5mRBfndDnCZ+7f4IMrVxWJ67J55/0DUaisOno2o+zboUckySmYrjLlLQ/q7FcaX 1pRgSPjgff/KLTnYkJgnU4gkvyg50Re5gStzPT3KMJvZhbxpjIIo8zYj3nOEx38= =Xloy -----END PGP SIGNATURE-----