fix for #227. Force re-install of fiona #229
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I'm going to hold off on merging this because I think Fiona is being installed twice. If you run the image and immediately uninstall fiona with I know it is explicitly pip installed but I also believe it's being installed from conda-forge somewhere. Maybe as a dependency of another package? I'll take a look at the build log and see if I can find something. |
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Looks like Fiona is indeed installed a second time from conda-forge by this command: We tend to prefer conda installations so I will try removing the pip install lines and see what happens |
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I tried to remove the pip install of fiona, but it didn’t fix the error.
…On Mon, Jul 9, 2018 at 2:19 PM crawforc3 ***@***.***> wrote:
Looks like Fiona is indeed installed a second time from conda-forge by
this command:
conda install -y -c conda-forge -c ioam holoviews geoviews && \
We tend to prefer conda installations so I will try removing the pip
install lines and see what happens
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Yeah, you're right. I just got the same error. Found this issue which was never resolved: conda-forge/fiona-feedstock#65 The command |
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I think geopandas has a fiona dependency, but some of the other packages
may as well.
One thing that I encountered that may be helpful, when I first started
looking into this issue, I noticed that I had to ‘pip uninstall fiona’
twice before it would completely uninstall. I didn’t try using conda to
uninstall it, as you did, because I’m less familiar with conda. Don’t know
if that offers a clue to the solution, but it’s something I found to be
odd.
…On Mon, Jul 9, 2018 at 4:16 PM crawforc3 ***@***.***> wrote:
Yeah, you're right. I just got the same error.
Found this issue which was never resolved: conda-forge/fiona-feedstock#65
<conda-forge/fiona-feedstock#65>
The command conda install -y -c conda-forge -c ioam holoviews geoviews
installs a bunch of dependencies (including geopandas and fiona). It's
probably worth breaking that down into separate commands and/or finding an
alternative method to install whichever one has fiona as a dependency
Jul 09 14:07:06 The following NEW packages will be INSTALLED:
Jul 09 14:07:06
Jul 09 14:07:06 boost: 1.67.0-py36h3e44d54_0 conda-forge
Jul 09 14:07:06 boost-cpp: 1.67.0-h3a22d5f_0 conda-forge
Jul 09 14:07:06 cartopy: 0.16.0-py36_0 conda-forge
Jul 09 14:07:06 click-plugins: 1.0.3-py_1 conda-forge
Jul 09 14:07:06 cligj: 0.4.0-py36_0 conda-forge
Jul 09 14:07:06 descartes: 1.1.0-py_1 conda-forge
Jul 09 14:07:06 fiona: 1.7.12-py36_0 conda-forge
Jul 09 14:07:06 freexl: 1.0.5-hf837533_1 conda-forge
Jul 09 14:07:06 gdal: 2.2.2-py36hc209d97_1
Jul 09 14:07:06 geopandas: 0.3.0-py_1 conda-forge
Jul 09 14:07:06 geoviews: 1.5.1-py_0 conda-forge
Jul 09 14:07:06 geoviews-core: 1.5.1-py_1 conda-forge
Jul 09 14:07:06 giflib: 5.1.4-h470a237_0 conda-forge
Jul 09 14:07:06 hdf4: 4.2.13-0 conda-forge
Jul 09 14:07:06 holoviews: 1.10.7-py_0 conda-forge
Jul 09 14:07:06 json-c: 0.12.1-0 conda-forge
Jul 09 14:07:06 kealib: 1.4.8-hfc679d8_0 conda-forge
Jul 09 14:07:06 krb5: 1.16.1-hbb41f41_0 conda-forge
Jul 09 14:07:06 libdap4: 3.19.1-0 conda-forge
Jul 09 14:07:06 libgdal: 2.2.2-h804cdde_1
Jul 09 14:07:06 libgfortran: 3.0.0-1
Jul 09 14:07:06 libkml: 1.3.0-hfce3912_7 conda-forge
Jul 09 14:07:06 libnetcdf: 4.4.1.1-10 conda-forge
Jul 09 14:07:06 libpq: 10.3-h1ad7b7a_0
Jul 09 14:07:06 libspatialindex: 1.8.5-hfc679d8_2 conda-forge
Jul 09 14:07:06 libspatialite: 4.3.0a-h72746d6_18
Jul 09 14:07:06 munch: 2.3.2-py_0 conda-forge
Jul 09 14:07:06 netcdf4: 1.3.1-py36_1 conda-forge
Jul 09 14:07:06 openjpeg: 2.3.0-2 conda-forge
Jul 09 14:07:06 owslib: 0.16.0-py_0 conda-forge
Jul 09 14:07:06 poppler: 0.60.1-hc909a00_0
Jul 09 14:07:06 poppler-data: 0.4.9-0 conda-forge
Jul 09 14:07:06 psycopg2: 2.7.5-py36_0 conda-forge
Jul 09 14:07:06 pyepsg: 0.3.2-py_1 conda-forge
Jul 09 14:07:06 pyproj: 1.9.5.1-py36_0 conda-forge
Jul 09 14:07:06 pysal: 1.14.3-py36_0 conda-forge
Jul 09 14:07:06 pyshp: 1.2.12-py_0 conda-forge
Jul 09 14:07:06 pyviz_comms: 0.1.1-py_0 conda-forge
Jul 09 14:07:06 rtree: 0.8.3-py36_0 conda-forge
Jul 09 14:07:06 shapely: 1.6.4-py36h164cb2d_1 conda-forge
Jul 09 14:07:06 util-linux: 2.21-0
Jul 09 14:07:06 xerces-c: 3.2.1-h5d6a6da_1 conda-forge
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Thanks, I noticed that too. It's because there are two versions installed -- one by pip and one by conda (pip can uninstall both). Textbook case of why it can be problematic to use pip and conda :) |
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Any luck tracking down a good solution to this issue? ...as opposed to my hacky suggestion |
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I haven't found a better solution yet. If I don't make progress today I will add your temporary fix until I can get something permanent figured out. |
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Has there been any progress? I cannot import geopandas for the PASSNYC competition |
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@wesg52 |
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@crawforc3 I don't have any ideas on how to fix the tensorflow issue, but FWIW I will say that I encountered errors building Tensorflow on Mac OSX, but everything built properly (albeit with a LOT of warnings) once I switched to a Debian-based linux distro. |
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Thanks @askingalot - we're already running a Debian-based image. I opened this issue with TF tensorflow/tensorflow#20938 |
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Whew. Finally got this fixed! |
ghost
closed this
2 participants
Fix for #227. Geopandas was failing because there was an
ImportErrorwhen importing fiona. Doing apip install -I fionafixes the issue.