You were right - I had two gdals, a manual installation and an installation from apt* and this confused my system.
So this is what I did: 1. Removed packages 'gdal-bin', 'libgdal-dev' etc using: sudo apt-get purge --auto-remove gdal-bin sudo apt-get purge --auto-remove libgdal sudo apt-get purge --auto-remove libkml-dev 2. Manually removed files from '/usr/local' e.g.: sudo find /usr/local/bin/ -name 'gdal*' -delete sudo find /usr/local/lib/ -name 'libgdal*' -delete After that rgdal installs without a problem. I am surprised that I had to manually delete files from the disk (I guess manual install means manual deletion?), but yes this does solve the problem. Many thanks Edzer and Roger! On 04/08/16 19:13, Edzer Pebesma wrote: > What is your output of gdal-config --libs ? On 14.04 I see: > > $ gdal-config --libs > -L/usr/local/lib -lgdal > $ which gdal-config > /usr/local/bin/gdal-config > $ gdal-config --version > 2.1.0 > > which indicates a manual install (from source). Your error message below > indicates a version in /usr/local/ that is broken. Manually installed > libs in /usr/local override the ones installed by apt* (which are in > /usr/lib etc -- Robin's post assumes no installs in /usr/local), so now > you must either: > > 1. fix the installed version in /usr/local , or > 2. remove the ones installed in /usr/local so that the ones in /usr/lib > are found. > > On 04/08/16 16:42, Tomislav Hengl wrote: >> Hi Roger, >> >> Thanks for this. I was looking at this post by Robin >> (https://www.r-bloggers.com/installing-rgdal-in-ubuntu-13-04/) and I >> followed all steps but I still get the same results. Should I remove all >> packages connected with GDAL and then start with installing from >> scratch? How do I find double installations / broken links? I've tested >> gdal utils from command line and everything works fine BTW. >> >> Here is what I get when I check when I look for gdal on my server: >> >> $ sudo apt-cache pkgnames|grep -i gdal >> libgdal1i >> libgdal-java >> libgdal1-1.11.3-grass >> libgdal1-dev >> libgdal-dev >> libgdal-doc >> libgdal-perl >> gdal-bin >> python3-gdal >> python-gdal >> dans-gdal-scripts >> >> Thank you >> >> >> On 03/08/16 23:00, Roger Bivand wrote: >>> Hi Tom, >>> >>> As you can see from the configure output, your GDAL install is broken: >>> >>> ... >>> checking gdal.h usability... yes >>> checking gdal.h presence... yes >>> checking for gdal.h... yes >>> checking gdal: linking with --libs only... no >>> checking gdal: linking with --libs and --dep-libs... no >>> /usr/local/lib/libgdal.so: undefined reference to >>> `kmlengine::Href::Parse(std::__cxx11::basic_string<char, >>> std:: char_traits<char>, std::allocator<char> > const&)' >>> /usr/local/lib/libgdal.so: undefined reference to >>> `kmlengine::KmzFile::ReadKmlAndGetPath(std::__cxx11::basic_string<char, >>> std:: char_traits<char>, std::allocator<char> >*, >>> std: :__cxx11::basic_string<char, std::char_traits<char>, >>> std:: allocator<char> >*) const' >>> ... >>> >>> My guess is either multiple installed GDAL versions, or a GDAL built >>> with libkml but without access to the libkml shared object. With >>> correctly installed GDAL, you would see: >>> >>> checking gdal.h usability... yes >>> checking gdal.h presence... yes >>> checking for gdal.h... yes >>> checking gdal: linking with --libs only... yes >>> >>> It could also be a C++ version problem between GDAL and its >>> dependencies, but I suspect a broken GDAL. >>> >>> Hope this helps, >>> >>> Roger >>> >>> On Wed, 3 Aug 2016, Tomislav Hengl wrote: >>> >>>> Hi Roger, >>>> >>>> I am sorry to bother you with this. I have reinstalled R on my server >>>> (actually MRO) and I have been stuck now trying to install rgdal >>>> (constantly getting "configure: Install failure: compilation and/or >>>> linkage problems. configure: error: GDALAllRegister not found in >>>> libgdal."). I've looked at numerous posts >>>> (http://stackoverflow.com/questions/34442010/r-cannot-install-rgdal-package-on-ubuntu-14-04) >>>> but I do not see where the problem comes from. >>>> >>>> Thank you! >>>> >>>> Here is my existing GDAL installation: >>>> >>>> $ gdal-config --version >>>> 2.1.0 >>>> $ proj >>>> Rel. 4.9.2, 08 September 2015 >>>> usage: proj [ -beEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ] >>>> >>>> $ ldd /usr/lib64/MRO-3.3.0/R-3.3.0/lib/R/bin/exec/R >>>> linux-vdso.so.1 => (0x00007ffd9098e000) >>>> libR.so => not found >>>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 >>>> (0x00007f8cebcb3000) >>>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 >>>> (0x00007f8ceb8e9000) >>>> /lib64/ld-linux-x86-64.so.2 (0x000055aff5b57000) >>>> >>>> >>>>> install.packages("rgdal") >>>> Installing package into ‘/home/tom/R/x86_64-pc-linux-gnu-library/3.3’ >>>> (as ‘lib’ is unspecified) >>>> trying URL >>>> 'https://mran.microsoft.com/snapshot/2016-06-01/src/contrib/rgdal_1.1-10.tar.gz' >>>> Content type 'application/octet-stream' length 1653393 bytes (1.6 MB) >>>> ================================================== >>>> downloaded 1.6 MB >>>> >>>> * installing *source* package ‘rgdal’ ... >>>> ** package ‘rgdal’ successfully unpacked and MD5 sums checked >>>> configure: CC: gcc -std=gnu99 >>>> configure: CXX: g++ >>>> configure: rgdal: 1.1-10 >>>> checking for /usr/bin/svnversion... yes >>>> configure: svn revision: 622 >>>> checking for gdal-config... /usr/local/bin/gdal-config >>>> checking gdal-config usability... yes >>>> configure: GDAL: 2.1.0 >>>> checking GDAL version >= 1.6.3... yes >>>> configure: experimental conditional use of GDAL2 >>>> checking for gcc... gcc -std=gnu99 >>>> checking whether the C compiler works... yes >>>> checking for C compiler default output file name... a.out >>>> checking for suffix of executables... >>>> checking whether we are cross compiling... no >>>> checking for suffix of object files... o >>>> checking whether we are using the GNU C compiler... yes >>>> checking whether gcc -std=gnu99 accepts -g... yes >>>> checking for gcc -std=gnu99 option to accept ISO C89... none needed >>>> checking how to run the C preprocessor... gcc -std=gnu99 -E >>>> checking for grep that handles long lines and -e... /bin/grep >>>> checking for egrep... /bin/grep -E >>>> checking for ANSI C header files... yes >>>> checking for sys/types.h... yes >>>> checking for sys/stat.h... yes >>>> checking for stdlib.h... yes >>>> checking for string.h... yes >>>> checking for memory.h... yes >>>> checking for strings.h... yes >>>> checking for inttypes.h... yes >>>> checking for stdint.h... yes >>>> checking for unistd.h... yes >>>> checking gdal.h usability... yes >>>> checking gdal.h presence... yes >>>> checking for gdal.h... yes >>>> checking gdal: linking with --libs only... no >>>> checking gdal: linking with --libs and --dep-libs... no >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::Href::Parse(std::__cxx11::basic_string<char, std:: >>>> char_traits<char>, std::allocator<char> > const&)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::KmzFile::ReadKmlAndGetPath(std::__cxx11::basic_string<char, >>>> std:: char_traits<char>, std::allocator<char> >*, std: >>>> :__cxx11::basic_string<char, std::char_traits<char>, std:: >>>> allocator<char> >*) const' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::KmzFile::OpenFromString(std::__cxx11::basic_string<char, >>>> std:: char_traits<char>, std::allocator<char> > const&)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmldom::SerializePretty[abi:cxx11](boost::intrusive_ptr<kmldom::Element> >>>> const&)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmldom::Parse(std::__cxx11::basic_string<char, >>>> std::char_traits<char>, std:: allocator<char> > const&, >>>> std::__cxx11::basic_string<char, std:: char_traits<char>, >>>> std::allocator<char> >*)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::KmzFile::ReadFile(char const*, std: >>>> :__cxx11::basic_string<char, std::char_traits<char>, std:: >>>> allocator<char> >*) const' >>>> collect2: error: ld returned 1 exit status >>>> /usr/bin/ld: warning: libproj.so.10, needed by >>>> /usr/local/lib/libgdal.so, may conflict with libproj.so.9 >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::Href::Parse(std::__cxx11::basic_string<char, std:: >>>> char_traits<char>, std::allocator<char> > const&)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::KmzFile::ReadKmlAndGetPath(std::__cxx11::basic_string<char, >>>> std:: char_traits<char>, std::allocator<char> >*, std: >>>> :__cxx11::basic_string<char, std::char_traits<char>, std:: >>>> allocator<char> >*) const' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::KmzFile::OpenFromString(std::__cxx11::basic_string<char, >>>> std:: char_traits<char>, std::allocator<char> > const&)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmldom::SerializePretty[abi:cxx11](boost::intrusive_ptr<kmldom::Element> >>>> const&)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmldom::Parse(std::__cxx11::basic_string<char, >>>> std::char_traits<char>, std:: allocator<char> > const&, >>>> std::__cxx11::basic_string<char, std:: char_traits<char>, >>>> std::allocator<char> >*)' >>>> /usr/local/lib/libgdal.so: undefined reference to >>>> `kmlengine::KmzFile::ReadFile(char const*, std: >>>> :__cxx11::basic_string<char, std::char_traits<char>, std:: >>>> allocator<char> >*) const' >>>> collect2: error: ld returned 1 exit status >>>> configure: Install failure: compilation and/or linkage problems. >>>> configure: error: GDALAllRegister not found in libgdal. >>>> ERROR: configuration failed for package ‘rgdal’ >>>> * removing ‘/home/tom/R/x86_64-pc-linux-gnu-library/3.3/rgdal’ >>>> >>>> >>>> >> _______________________________________________ >> R-sig-Geo mailing list >> R-sig-Geo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo [[alternative HTML version deleted]] _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo