Down the `rgdal` rabbit hole

Down, down, down

I have a package that depends on INLA, which has recently begun failing to load if rgdal isn’t installed correctly. rgdal can’t be installed without the GDAL library, which requires PROJ, which requires SQLite. I needed to install all of these on our cluster without root access. That meant compiling each one to a non-standard location, then ensuring that the next in the sequence knew where this was. It also meant that if I missed an option in, say SQLite, I had to start from the bottom and recompile everything.

Clawing my way out

This is what I eventually (after 2 days of work) got to work.


  1. Download and untar the most recent SQLite amalgamation. I did not use the autoconf version.
  2. Configure:
./configure --prefix=/usr/lusers/jkbest/inst/sqlite-3.33.0 \

Note the CFLAGS here. Without that rgdal will fail to install with a message about table_columns or similar and you’ll need to start over from this step (ask me how I know!).

  1. Compile and install:
make -jN
make install
  1. Update $PATHs. In your .zshrc, .bashrc or similar, add entries to PATH for bin, LD_LIBRARY_PATH for lib, CPATH for include, and PKG_CONFIG_PATH for lib/pkgconfig. I don’t know which of these mattered, but it didn’t hurt to add them.


  1. Download and untar the latest version of PROJ.

  2. Configure:

./configure --prefix=$INSTALL_PATH/proj-7.2.0 \
    SQLITE3_CFLAGS=-I/usr/lusers/jkbest/inst/sqlite-3.33.0/include \
    SQLITE3_LIBS="-L/usr/lusers/jkbest/inst/sqlite-3.33.0/lib -lsqlite3" \
    CPPFLAGS=-I/usr/lusers/jkbest/inst/sqlite-3.33.0/include \
    LDFLAGS="-L/usr/lusers/jkbest/inst/sqlite-3.33.0/lib -lsqlite3"

  1. Compile and install:
make install
  1. Update PATH, LD_LIBRARY_PATH, PKG_CONFIG_PATH, and CPATH as described above.


  1. Download and untar the latest version of GDAL.

  2. Configure:

./configure --prefix=/usr/lusers/jkbest/inst/gdal-3.2.0\
    CFLAGS="-I/usr/lusers/jkbest/inst/proj-7.2.0/include -I/usr/lusers/jkbest/inst/sqlite-3.33.0/include"\
    LIBS="-L/usr/lusers/jkbest/inst/proj-7.2.0/lib -lproj -L/usr/lusers/jkbest/inst/sqlite-3.33.0/lib -lsqlite3" \
    CPPFLAGS="-I/usr/lusers/jkbest/inst/proj-7.2.0/include -I/usr/lusers/jkbest/inst/sqlite-3.33.0/include"\
    LDFLAGS="-L/usr/lusers/jkbest/inst/proj-7.2.0/lib -lproj -L/usr/lusers/jkbest/inst/sqlite-3.33.0/lib -lsqlite3"
  1. Compile and install (takes a while and benefits from multiple jobs):
make -jN
make install
  1. Update environmental variables.


In R, run

install.packages("rgdal", configure.args = "--host=host")

No idea why the host argument is necessary, but it errors with messages about cross-compiling if it is not included.

Fresh air

That was easy, right?

John K Best
John K Best
PhD candidate

My research focuses on advancing the use of statistics in ecology and fisheries.