How to fix 'libproj not found in standard or given locations' error in r

Question

I'm trying to install the 'agricolae' package on R, but I get an error saying

    configure: error: libproj not found in standard or given locations.
    ERROR: configuration failed for package ‘sf’
    * removing ‘/R/x86_64-pc-linux-gnu-library/3.6/sf’
    Warning in install.packages :
      installation of package ‘sf’ had non-zero exit status
    ERROR: dependency ‘sf’ is not available for package ‘spdep’
    * removing ‘/R/x86_64-pc-linux-gnu-library/3.6/spdep’
    Warning in install.packages :
      installation of package ‘spdep’ had non-zero exit status
    ERROR: dependency ‘spdep’ is not available for package ‘agricolae’
    * removing ‘/R/x86_64-pc-linux-gnu-library/3.6/agricolae’
    Warning in install.packages :
      installation of package ‘agricolae’ had non-zero exit status

I recently upgraded to Ubuntu 18.04.2 and R version 3.6.0 (2019-04-26) -- "Planting of a Tree" and that's when the problems started.

When I do

    $ sudo apt-get install -y libproj-dev

I get:

    libproj-dev is already the newest version (5.2.0-1~bionic0).

Answer 1

The error says that package 'sf' is not available for dependency 'spdep'. So you should be attempting to install pkg 'sf'. (I'm on the same OS as you and pkg:agricolae installed without problem just now. I have a more complete set of spatial R and system packages than you do.)

Edit: There have been reports that it was necessary in addressing this problem to create an environment link to the location of your libraries:

$ export LD_LIBRARY_PATH=/lib:/usr/lib:/usr/local/lib 

(From: https://stat.ethz.ch/pipermail/r-sig-geo/2018-August/026740.html which in turn linked to https://gis.stackexchange.com/questions/157059/repairing-broken-gdal-and-proj-4-on-ubuntu, which has so further debugging options mentioned.)