error importing geopandas (libmfhdf.so.0 not found)

[zogg]

I have miniconda3 on an Ubuntu 64-bit system.
I installed geopandas from conda-forge, which affected conda and conda-env:
 conda:           4.3.18-py36_0                  --> 4.2.13-py36_0 conda-forge
 conda-env:       2.6.0-0                        --> 2.6.0-0       conda-forge

When I try to import geopandas, I get

---> 9 from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: libmfhdf.so.0: cannot open shared object file: No such file or directory

I tried installing hdf4 and h5py, but that didn't solve the problem.

Here's my conda list output, am I missing some required packages for geopandas?

asn1crypto                0.22.0                   py36_0    defaults
bleach                    1.5.0                    py36_0    defaults
bokeh                     0.12.5                   py36_0    defaults
bzip2                     1.0.6                         3    defaults
cairo                     1.14.8                        0    defaults
cffi                      1.10.0                   py36_0    defaults
click                     6.7                      py36_0    defaults
click-plugins             1.0.3                    py36_0    defaults
cligj                     0.4.0                    py36_0    defaults
conda                     4.2.13                   py36_0    conda-forge
conda-env                 2.6.0                         0    conda-forge
cryptography              1.8.1                    py36_0    defaults
curl                      7.49.0                        1    defaults
cycler                    0.10.0                   py36_0    defaults
dbus                      1.10.10                       0    defaults
decorator                 4.0.11                   py36_0    defaults
descartes                 1.1.0                    py36_0    conda-forge
entrypoints               0.2.2                    py36_1    defaults
expat                     2.1.0                         0    defaults
fiona                     1.7.6               np112py36_0    conda-forge
fontconfig                2.12.1                        3    defaults
freetype                  2.5.5                         2    defaults
freexl                    1.0.2                         1    conda-forge
gdal                      2.1.3               np112py36_0    conda-forge
geopandas                 0.2.1                    py36_3    conda-forge
geos                      3.5.0                         0    defaults
giflib                    5.1.4                         0    conda-forge
glib                      2.50.2                        1    defaults
gmp                       6.1.0                         0    defaults
gsl                       2.2.1                         0    defaults
gst-plugins-base          1.8.0                         0    defaults
gstreamer                 1.8.0                         0    defaults
h5py                      2.7.0               np112py36_0    defaults
harfbuzz                  0.9.39                        2    defaults
hdf4                      4.2.11                        0    defaults
hdf5                      1.8.17                        1    defaults
html5lib                  0.999                    py36_0    defaults
icu                       54.1                          0    defaults
idna                      2.5                      py36_0    defaults
ipykernel                 4.6.1                    py36_0    defaults
ipython                   6.0.0                    py36_1    defaults
ipython_genutils          0.2.0                    py36_0    defaults
ipywidgets                6.0.0                    py36_0    defaults
jbig                      2.1                           0    defaults
jedi                      0.10.2                   py36_2    defaults
jinja2                    2.9.6                    py36_0    defaults
jpeg                      9b                            0    defaults
json-c                    0.12                          0    conda-forge
jsonschema                2.6.0                    py36_0    defaults
jupyter                   1.0.0                    py36_3    defaults
jupyter_client            5.0.1                    py36_0    defaults
jupyter_console           5.1.0                    py36_0    defaults
jupyter_core              4.3.0                    py36_0    defaults
kealib                    1.4.6                         0    defaults
krb5                      1.13.2                        0    defaults
libdap4                   3.18.3                        2    conda-forge
libffi                    3.2.1                         1    defaults
libgcc                    5.2.0                         0    defaults
libgfortran               3.0.0                         1    defaults
libiconv                  1.14                          0    defaults
libnetcdf                 4.4.1                         0    defaults
libpng                    1.6.27                        0    defaults
libpq                     9.5.4                         0    defaults
libsodium                 1.0.10                        0    defaults
libspatialindex           1.8.5                         1    conda-forge
libspatialite             4.3.0a                       14    conda-forge
libtiff                   4.0.6                         3    defaults
libxcb                    1.12                          1    defaults
libxml2                   2.9.4                         0    defaults
markupsafe                0.23                     py36_2    defaults
matplotlib                2.0.2               np112py36_0    defaults
mistune                   0.7.4                    py36_0    defaults
mkl                       2017.0.1                      0    defaults
munch                     2.1.0                    py36_0    defaults
nbconvert                 5.1.1                    py36_0    defaults
nbformat                  4.3.0                    py36_0    defaults
ncurses                   5.9                          10    defaults
notebook                  5.0.0                    py36_0    defaults
numpy                     1.12.1                   py36_0    defaults
openjpeg                  2.1.2                         2    conda-forge
openssl                   1.0.2k                        2    defaults
packaging                 16.8                     py36_0    defaults
pandas                    0.20.1              np112py36_0    defaults
pandoc                    1.15.0.6                      0    defaults
pandocfilters             1.4.1                    py36_0    defaults
pango                     1.40.3                        1    defaults
path.py                   10.3.1                   py36_0    defaults
pcre                      8.39                          1    defaults
pexpect                   4.2.1                    py36_0    defaults
pickleshare               0.7.4                    py36_0    defaults
pip                       9.0.1                    py36_1    defaults
pixman                    0.34.0                        0    defaults
proj4                     4.9.3                         3    conda-forge
prompt_toolkit            1.0.14                   py36_0    defaults
psycopg2                  2.7.1                    py36_0    defaults
ptyprocess                0.5.1                    py36_0    defaults
py4j                      0.10.4                   py36_0    conda-forge
pyasn1                    0.2.3                    py36_0    defaults
pycosat                   0.6.2                    py36_0    defaults
pycparser                 2.17                     py36_0    defaults
pygments                  2.2.0                    py36_0    defaults
pyopenssl                 17.0.0                   py36_0    defaults
pyparsing                 2.1.4                    py36_0    defaults
pyproj                    1.9.5.1                  py36_0    defaults
pyqt                      5.6.0                    py36_2    defaults
pysal                     1.13.0                   py36_0    defaults
pyspark                   2.1.1                    py36_0    conda-forge
python                    3.6.1                         2    defaults
python-dateutil           2.6.0                    py36_0    defaults
pytz                      2017.2                   py36_0    defaults
pyyaml                    3.12                     py36_0    defaults
pyzmq                     16.0.2                   py36_0    defaults
qt                        5.6.2                         4    defaults
qtconsole                 4.3.0                    py36_0    defaults
readline                  6.2                           2    defaults
requests                  2.14.2                   py36_0    defaults
rtree                     0.8.3                    py36_0    conda-forge
ruamel_yaml               0.11.14                  py36_1    defaults
scipy                     0.19.0              np112py36_0    defaults
setuptools                27.2.0                   py36_0    defaults
shapely                   1.5.17              np112py36_2    conda-forge
simplegeneric             0.8.1                    py36_1    defaults
sip                       4.18                     py36_0    defaults
six                       1.10.0                   py36_0    defaults
sqlalchemy                1.1.9                    py36_0    defaults
sqlite                    3.13.0                        0    defaults
terminado                 0.6                      py36_0    defaults
testpath                  0.3                      py36_0    defaults
tk                        8.5.18                        0    defaults
tornado                   4.5.1                    py36_0    defaults
traitlets                 4.3.2                    py36_0    defaults
util-linux                2.21                          0    defaults
wcwidth                   0.1.7                    py36_0    defaults
wheel                     0.29.0                   py36_0    defaults
widgetsnbextension        2.0.0                    py36_0    defaults
xerces-c                  3.1.4                         0    defaults
xz                        5.2.2                         1    defaults
yaml                      0.1.6                         0    defaults
zeromq                    4.1.5                         0    defaults
zlib                      1.2.8                         3    defaults



 -Thanks, zogg

[Paul Hobson]

Fiona is what's having trouble as your error message states.

Can you try in a fresh environment?

$ conda create --name=gis python=3.6 fiona

$ source activate gis

(gis)$ python -c "import fiona; print(fiona.__version__)"

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[zogg]

That conda-create command resulted in


UnsatisfiableError: The following specifications were found to be in conflict:
  - fiona -> gdal 1.10.1 -> numpy 1.8* -> python 2.6* -> openssl 1.0.1*
  - python 3.6*


 -zogg

[Paul Hobson]

I wouldn't expect python 2.6 to work. You need to use Python 3.5 or greater. I did leave off a crucial component though. You need to specify the channel as conda-forge:

$ conda create --name=gis python=3.6 fiona --channel=conda-forge

$ source activate gis

(gis)$ python -c "import fiona; print(fiona.__version__)"

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[zogg]

That command worked. Fiona version is 1.7.6.
I was also able to install geopandas from conda-forge and import it in the new environment.

(gis)$ python -c "import geopandas; print(geopandas.__version__)"
0.2.1

In the new env, python -V is
3.6.1
not
Python 3.6.1 :: Continuum Analytics, Inc.
does that matter?

Do I have to use a different environment for installing conda-forge packages vs regular conda packages?

 -Thanks, zogg