Various changes in gdal compilation and structure (#17)

* Various changes in gdal compilation and structure

- Add dependencies to compile as homebrew gdal2 does
  https://github.com/OSGeo/homebrew-osgeo4mac/blob/master/Formula/gdal2.rb
- Add configure options to gdal to compile as homebrew gdal2 does
- change structure slightly so that debugging is easier
- add missing definition for $MRAN

* Add odbc and curl to gdal

* Cleanup to remove external libraries

* Dependencies changed

* Move to gdal 2.1.3 and add KML support

- add some structure to dependencies

* Add LD_LIBRARY_PATH

* Fix HDF5 support

Error in detection HDF5 libraries in 2.1 branch - see
http://permalink.gmane.org/gmane.comp.gis.gdal.devel/44474 for info.

* Fixed Typo for HDF5 library location

Thanks Edzer

geospatial/Dockerfile

 FROM rocker/tidyverse:latest
 MAINTAINER "Carl Boettiger" cboettig@ropensci.org
 
-ENV GDAL_VERSION 2.1.2
-ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH 
+ENV GDAL_VERSION 2.1.3
+ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
-## Add LaTeX, rticles and bookdown support
-RUN echo "deb-src http://deb.debian.org/debian jessie main" >> /etc/apt/sources.list \
+RUN wget http://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION}.tar.gz \
+  && tar -xf gdal-${GDAL_VERSION}.tar.gz \
+## Install dependencies of gdal-$GDAL_VERSION
+## && echo "deb-src http://deb.debian.org/debian jessie main" >> /etc/apt/sources.list \
   && apt-get update \
-  && apt-get build-dep -y -o APT::Get::Build-Dep-Automatic=true libgdal-dev \
+##  && apt-get build-dep -y -o APT::Get::Build-Dep-Automatic=true libgdal-dev \
   && apt-get install -y --no-install-recommends \
-  libgeos-dev \
+  # libpng12-dev \
+  # libjpeg-dev \
+  # libgif-dev \
+  # libtiff-dev \
+  # libgeotiff-dev \
   libproj-dev \
-  libudunits2-dev \
-  && wget http://download.osgeo.org/gdal/${GDAL_VERSION}/gdal-${GDAL_VERSION}.tar.gz \
-  && tar -xf gdal-${GDAL_VERSION}.tar.gz \
+  libgeos-dev \
+  libhdf4-alt-dev \
+  libhdf5-dev \
+  libsqlite3-dev \
+  libfreexl-dev \
+  unixodbc-dev \
+  libexpat1-dev \
+  libxerces-c-dev \
+  libnetcdf-dev \
+  libudunits2-dev \ 
+  libkml-dev \
+## Configure options based on homebrew gdal2 https://github.com/OSGeo/homebrew-osgeo4mac/blob/master/Formula/gdal2.rb
   && cd gdal* \
-  && ./configure && make && make install \
+  && ./configure \
+    --with-geotiff \
+    --with-sqlite3 \
+    --with-freexl \
+    --with-spatialite \
+    --with-geos \
+    --with-hdf4 \
+    --with-hdf5=/usr/lib/x86_64-linux-gnu/hdf5/serial \
+    --with-libjson-c \
+    --with-netcdf \
+    --with-odbc \
+    --with-curl \
+    --without-grass \
+    --without-libgrass \
+  && make \
+  && make install \
   && cd .. && rm -rf gdal-* \
   && . /etc/environment \
-  ## Install R packages labeled "core" in Spatial taskview 
+## Install R packages labeled "core" in Spatial taskview 
   && install2.r --error --repos $MRAN \
     classInt \
     DCluster \
     deldir \
     dggridR \
-#    geoR \ ## Needs R built with tcl/tk support 
+#       geoR \ ## Needs R built with tcl/tk support 
     gstat \
     maptools \
     RandomFields \
@@ -38,5 +68,4 @@ RUN echo "deb-src http://deb.debian.org/debian jessie main" >> /etc/apt/sources.
     spatstat \
     spdep \
     splancs
-
-
+    
\ No newline at end of file