More trouble Installing rgdal on ubuntu 16.04

Question

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

Answer 1

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.