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

[Tomislav Hengl]

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’
>>
>>
>>
>