This problem installing rgdal is not resolved in other similar questions already posted. I installed gdal using the advice on http://www.sarasafavi.com/installing-gdalogr-on-ubuntu.html and also decribed in other answers like this trouble in installing rgdal on ubuntu 16.04 that means from ppa:ubuntugis.
Then when I try to install rgdal the following error appears
> install.packages("rgdal")
Installing package into ‘/home/leonardo/R/x86_64-pc-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/rgdal_1.3-4.tar.gz'
Content type 'application/x-gzip' length 1664774 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
* installing *source* package ‘rgdal’ ...
** package ‘rgdal’ successfully unpacked and MD5 sums checked
configure: R_HOME: /usr/lib/R
configure: CC: gcc -std=gnu99
configure: CXX: g++
configure: C++11 support available
configure: rgdal: 1.3-4
checking for /usr/bin/svnversion... no
configure: svn revision: 766
checking for gdal-config... /home/leonardo/anaconda3/bin/gdal-config
checking gdal-config usability... yes
configure: GDAL: 2.2.2
checking GDAL version >= 1.11.4... yes
checking gdal: linking with --libs only... no
checking gdal: linking with --libs and --dep-libs... no
/usr/bin/x86_64-linux-gnu-ld: warning: libproj.so.12, needed by /home/leonardo/anaconda3/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/usr/bin/x86_64-linux-gnu-ld: warning: libpoppler.so.71, needed by /home/leonardo/anaconda3/lib/libgdal.so, not found (try using -rpath or -rpath-link)
/usr/bin/x86_64-linux-gnu-ld: warning: libxerces-c-3.2.so, needed by /home/leonardo/anaconda3/lib/libgdal.so,
...
500 lines more
...
/home/leonardo/anaconda3/lib/libgeos_c.so: undefined reference to `geos::geom::PrecisionModel::PrecisionModel(double)'
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/leonardo/R/x86_64-pc-linux-gnu-library/3.5/rgdal’
Warning in install.packages :
installation of package ‘rgdal’ had non-zero exit status
It seems to be a problem with python anaconda that I have previously installed, I removed the anaconda python gdal package using
conda remove gdal
But the problems persist
The only way to solve this was to completely remove anaconda installation, following the instructions on https://conda.io/docs/user-guide/install/linux.html#uninstalling-anaconda-or-miniconda with some minor modifications for ubuntu 16.04, you have to open a terminal and remove the anaconda install directory:
rm -rf ~/anaconda3
rm -rf ~/.condarc ~/.conda ~/.continuum
Edit ~/.bashrc to remove the anaconda directory from your PATH environment variable.
After that the installation of rgdal
install.packages("rgdal")
goes without problems.