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

Wed Aug 3 23:00:04 CEST 2016

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’
>
>
>

-- 
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand at nhh.no
http://orcid.org/0000-0003-2392-6140
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http://depsy.org/person/434412