Problems with installing rgdal on Ubuntu "checking gdal: linking with --libs only... no"

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?