Error while installing GDAL

On my MacBook, the update/fresh install of GDAL using this approach with homebrew worked out fine. The problem on my Mac was that I apparently had an old GDAL version installed and wasn't able to update with brew upgrade gdal because of the above error message.

Solution in short:

brew unlink gdal
brew tap osgeo/osgeo4mac && brew tap --repair
brew install jasper netcdf # gdal dependencies
brew install gdal2 --with-armadillo --with-complete --with-libkml --with-unsupported
brew link --force gdal2

Verification:

$> gdal-config --version
2.1.3
$> gdal-config --libs
-L/usr/local/Cellar/gdal2/2.1.3_3/lib -lgdal
$> gdal-config --cflags
-I/usr/local/Cellar/gdal2/2.1.3_3/include

I had to include the header files as well to successfully install gdal:

sudo pip3 install GDAL==$(gdal-config --version | awk -F'[.]' '{print $1"."$2}') --global-option=build_ext --global-option="-I/usr/include/gdal"

Note: Using Python 3 and gdal was already installed on centOS

pip install GDAL==$(gdal-config --version | awk -F'[.]' '{print $1"."$2}')

This is a copy-paste of this comment by nicerobot, that at this time received more up votes than all currently posted answers combined.

As far as I can tell, it asks pip to install the pip package of the same version as the installed gdal system package.

Check that you installed GDAL using this command

gdal-config --version

Then run this commands:

pip download="some_path" GDAL
cd some_path
tar -xvzf GDAL-<version>.tar.gz
cd GDAL-<version>
python setup.py build_ext --include-dirs=/usr/include/gdal/
python setup.py install