Update Dockerfile

1. Update the version of R to 4.2.1.
2. Added missing software such as proj, gdal, git and some libs to the apt-get install list.
3. Update the packages that R needs to install to be consistent with the latest instructions in README.md.
4. Installed missing R packages, such as ncdf4, raster, etc.
5. Replace the constants in the download and installation paths of GAMS with environment variables.
6. Update the version of GAMS to 40.2. As stated in README.md, "as the model benefits significantly of recent improvements in GAMS and CONOPT4 it is recommended to work with the most recent versions of both".

Note, as of September 2022, the latest GAMS version is 40.3, but this version has not been tested. It has been tested that MAgPIE works fine with GAMS 40.2.

Author: moulai

Dockerfile

@@ -1,9 +1,10 @@
-FROM rocker/r-ver:3.6.2
+FROM rocker/r-ver:4.2.1
 
 RUN mkdir /home/magpie
 COPY . /home/magpie/
 
 RUN apt-get update \
+ && apt-get upgrade -y \
  && apt-get install -y libpng-dev \
  && apt-get install -y libjpeg-dev \
  && apt-get install -y zlib1g-dev \
@@ -16,17 +17,30 @@ RUN apt-get update \
  && apt-get install -y fonts-inconsolata \
  && apt-get install -y pandoc \
  && apt-get install -y pandoc-citeproc \
+ && apt-get install -y libfontconfig1-dev \
+ && apt-get install -y libharfbuzz-dev \
+ && apt-get install -y libfribidi-dev \
+ && apt-get install -y libfreetype6-dev \
+ && apt-get install -y libtiff5-dev \
+ && apt-get install -y r-cran-ncdf4 \
+ && apt-get install -y netcdf-bin \
+ && apt-get install -y libnetcdf-dev \
+ && apt-get install -y proj-bin \
+ && apt-get install -y libproj-dev \
+ && apt-get install -y gdal-bin \
+ && apt-get install -y libgdal-dev \
+ && apt-get install -y texlive-latex-extra \
+ && apt-get install -y git \
  && fc-cache -fv
 
-
-
-
 RUN R -e "options(repos = \
   list(CRAN = 'https://cran.rstudio.com/',pik='https://rse.pik-potsdam.de/r/packages')); \
   install.packages(c('gdxrrw', \
            'ggplot2', \
+           'citation', \
            'curl', \
            'gdx', \
+           'gms', \
            'magclass', \
            'madrat', \
            'mip', \
@@ -36,10 +50,15 @@ RUN R -e "options(repos = \
            'lusweave', \
            'luscale', \
            'goxygen', \
-           'luplot'))"
+           'luplot', \
+           'yaml'))"
+
+RUN R -e "install.packages(c('ncdf4', \
+                             'raster'))"
 
 # Set GAMS version
-ENV LATEST=30.3.0
+ENV LATEST=40.2.0
+ENV LATEST_SHORT=40.2
 ENV GAMS_VERSION=${LATEST}
 
 # Set GAMS bit architecture, either 'x64_64' or 'x86_32'
@@ -56,14 +75,15 @@ RUN cd /opt/gams &&\
     ./gams.exe &&\
     rm -rf gams.exe
 
-COPY gamslice.txt /opt/gams/gams30.3_linux_x64_64_sfx/gamslice.txt
+COPY gamslice.txt /opt/gams/gams${LATEST_SHORT}_linux_${GAMS_BIT_ARC}_sfx/gamslice.txt
 # Add GAMS path to user env path
 RUN GAMS_PATH=$(dirname $(find / -name gams -type f -executable -print)) &&\
     ln -s $GAMS_PATH /usr/local/bin &&\
     echo "export PATH=\$PATH:$GAMS_PATH" >> ~/.bashrc &&\
+    echo "export GAMS_PATH=$GAMS_PATH" >> ~/.bashrc &&\
     cd $GAMS_PATH &&\
     ./gamsinst -a
 
-COPY gamslice.txt /opt/gams/gams30.3_linux_x64_64_sfx/gamslice.txt
+COPY gamslice.txt /opt/gams/gams${LATEST_SHORT}_linux_${GAMS_BIT_ARC}_sfx/gamslice.txt
 
 CMD  cd /home/magpie && Rscript start.R