[R-sig-Geo] Problems with installing rgdal on Ubuntu "checking gdal: linking with --libs only... no"

[Edzer Pebesma]

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’
>>>
>>>
>>>
>>
> 
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-- 
Edzer Pebesma
Institute for Geoinformatics  (ifgi),  University of Münster
Heisenbergstraße 2, 48149 Münster, Germany; +49 251 83 33081
Journal of Statistical Software:   http://www.jstatsoft.org/
Computers & Geosciences:   http://elsevier.com/locate/cageo/
Spatial Statistics Society http://www.spatialstatistics.info

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