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I need your help solving this particular problem.

I am trying to install the Rgdal package, but I can't seem to be able to get past the installation. The output seems fairly normal at first (as far as I can tell).

* 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... no
configure: svn revision: 622
checking for gdal-config... /afs/ics.muni.cz/software/R-3.0.3/bin/gdal- config
checking gdal-config usability... yes
configure: GDAL: 1.10.1
checking GDAL version >= 1.6.3... yes
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

And then it gives me a warning message:

/usr/bin/ld: warning: libhdf5.so.6, needed by /software/R-3.0.3 lib/libgdal.so, not found (try using -rpath or -rpath-link)

Then it continues with a long list of undefined references:

/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Dread'
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Dget_create_plist'
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Pclose'
/software/R-3.0.3/lib/libgdal.so: undefined reference to `H5Sget_simple_extent_ndims'

I would be eternally grateful for any help or suggestions as I don't really understand what went wrong. Looking this problem up did not yield any useful results.

captain.marketa
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    Are you under Linux? Try to install the `libhdf5-dev` system package (through `apt-get` if you under Debian/Ubuntu or `yum` otherwise) and then try to install `rgdal` again. – nicola Sep 19 '16 at 13:00
  • BTW: I would suggest to update your R version. Not that you need packages, which depend on a newer version of R than 3.0.3. – J_F Sep 19 '16 at 13:05
  • Possible duplicate of [rgdal package installation](http://stackoverflow.com/questions/15248815/rgdal-package-installation) – user20650 Sep 19 '16 at 16:04

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