libgcc-ng, libstdcxx-ng do exist in conda-forge. But they're for Linux only, not for macOS, Windows.

• conda-forge/libgcc-ng
• conda-forge/libstdcxx-ng

These two packages include libraries for gcc. For macOS, install gcc with homebrew. They are contained by the gcc package already.

brew install gcc

Bioconda as a channel depends on Conda Forge and so specifying bioconda as the only channel is incorrect. Instead, a proper specification for using the bioconda channel is

name: freebayes
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
 - freebayes=1.3.6

See the channel configuration in the Usage section.

If the point of the new env is to have geopandas in it, then let Conda know that right from the start and it can solve the dependencies upfront:

conda create -n gp python=2 geopandas

However, as @martinfleis points out, you may still have channel priority issues. Testing on a linux-64 platform, I was able to install geopandas=0.4.0 from anaconda channel alone, but to install geopandas=0.5.0 required both anaconda and conda-forge, and could be provided in either priority. In @martinfleis's testing, only giving conda-forge priority worked. Hence,

conda create -n gp -c conda-forge -c defaults --override-channels python=2 geopandas

would be the consensus command.

Note on Channel Priorities

It is possible to change channel priorities at the configuration level, as in @martinfleis's comment to OP, and in this case would make it so that the first command above works exactly like the second. However, one should only make such a change of it really coincides with your channel preferences - not to achieve a particular installation.

The alternative, as demonstrated in the second command above, is to temporarily specify channel priorities in a create or install command. In that command, -c conda-forge coming first gives it priority over -c defaults. The --override-channels flag disables whatever other channels you might have in permanent configuration settings.

Additionally, one can still specify individual packages to come from a particular channel by prefixing <channel>:: to the package name. For example, if in the second command, I still wanted to source Python from defaults, it would be defaults::python=2.

If you have more than a couple of exceptions that you want to specify, then it's probably time to consider installing from a YAML.