import error after clean install of fiona

问题:

I installed fiona as follows:

conda install -c conda-forge fiona

It installed without any errors. When I try to import fiona, I get the following error:

Traceback (most recent call last):

  File "<stdin>", line 1, in <module>
  File "/home/name/anaconda3/lib/python3.6/site-packages/fiona/__init__.py", line 69, in <module>
    from fiona.collection import Collection, BytesCollection, vsi_path
  File "/home/name/anaconda3/lib/python3.6/site-packages/fiona/collection.py", line 9, in <module>
    from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
ImportError: /home/name/anaconda3/lib/python3.6/site-packages/fiona/../../.././libkea.so.1.4.7: undefined symbol: _ZN2H56H5FileC1ERKSsjRKNS_17FileCreatPropListERKNS_15FileAccPropListE

Incase it helps with diagnosis, here is the output of conda list:

_ipyw_jlab_nb_ext_conf    0.1.0            py36he11e457_0
alabaster                 0.7.10           py36h306e16b_0
anaconda                  custom           py36hbbc8b67_0
anaconda-client           1.6.9                    py36_0
anaconda-navigator        1.7.0                    py36_0
anaconda-project          0.8.2            py36h44fb852_0
asn1crypto                0.24.0                   py36_0
astroid                   1.6.1                    py36_0
astropy                   2.0.3            py36h14c3975_0
attrs                     17.4.0                   py36_0
automat                   0.6.0                    py36_0    conda-forge
Automat                   0.6.0                     <pip>
babel                     2.5.3                    py36_0
backports                 1.0              py36hfa02d7e_1
backports.shutil_get_terminal_size 1.0.0            py36hfea85ff_2
beautifulsoup4            4.6.0            py36h49b8c8c_1
bitarray                  0.8.1            py36h14c3975_1
bkcharts                  0.2              py36h735825a_0
blaze                     0.11.3           py36h4e06776_0
bleach                    2.1.2                    py36_0
bokeh                     0.12.13          py36h2f9c1c0_0
boost                     1.66.0                   py36_1    conda-forge
boost-cpp                 1.66.0                        1    conda-forge
boto                      2.48.0           py36h6e4cd66_1
bottleneck                1.2.1            py36haac1ea0_0
bzip2                     1.0.6                h9a117a8_4
ca-certificates           2018.1.18                     0    conda-forge
cairo                     1.14.12              h77bcde2_0
certifi                   2018.1.18                py36_0    conda-forge
cffi                      1.11.4           py36h9745a5d_0
chardet                   3.0.4            py36h0f667ec_1
click                     6.7              py36h5253387_0
click-plugins             1.0.3                    py36_0    conda-forge
cligj                     0.4.0                    py36_0    conda-forge
cloudpickle               0.5.2                    py36_1
clyent                    1.2.2            py36h7e57e65_1
colorama                  0.3.9            py36h489cec4_0
conda                     4.3.34                   py36_0    conda-forge
conda-build               3.4.1                    py36_0
conda-env                 2.6.0                         0    conda-forge
conda-verify              2.0.0            py36h98955d8_0
constantly                15.1.0                     py_0    conda-forge
contextlib2               0.5.5            py36h6c84a62_0
cryptography              2.1.4            py36hd09be54_0
cssselect                 1.0.3                      py_0    conda-forge
curl                      7.58.0               h84994c4_0
cycler                    0.10.0           py36h93f1223_0
cython                    0.27.3           py36h1860423_0
cytoolz                   0.9.0            py36h14c3975_0
dask                      0.16.1                   py36_0
dask-core                 0.16.1                   py36_0
datashape                 0.5.4            py36h3ad6b5c_0
dbus                      1.12.2               hc3f9b76_1
decorator                 4.2.1                    py36_0
distributed               1.20.2                   py36_0
docutils                  0.14             py36hb0f60f5_0
entrypoints               0.2.3            py36h1aec115_2
et_xmlfile                1.0.1            py36hd6bccc3_0
expat                     2.2.5                he0dffb1_0
fastcache                 1.0.2            py36h14c3975_2
filelock                  2.0.13           py36h646ffb5_0
fiona                     1.7.11                   py36_3    conda-forge
flask                     0.12.2           py36hb24657c_0
flask-cors                3.0.3            py36h2d857d3_0
fontconfig                2.12.4               h88586e7_1
freetype                  2.8                  hab7d2ae_1
freexl                    1.0.5                         0    conda-forge
gdal                      2.2.2            py36hc209d97_1
geos                      3.6.2                         1    conda-forge
get_terminal_size         1.0.0                haa9412d_0
gevent                    1.2.2            py36h2fe25dc_0
giflib                    5.1.4                         0    conda-forge
glib                      2.53.6               h5d9569c_2
glob2                     0.6              py36he249c77_0
gmp                       6.1.2                h6c8ec71_1
gmpy2                     2.0.8            py36hc8893dd_2
graphite2                 1.3.10               hf63cedd_1
greenlet                  0.4.12           py36h2d503a6_0
gst-plugins-base          1.12.4               h33fb286_0
gstreamer                 1.12.4               hb53b477_0
h5py                      2.7.1            py36h3585f63_0
harfbuzz                  1.7.4                hc5b324e_0
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1               h9caa474_1
heapdict                  1.0.0                    py36_2
html5lib                  1.0.1            py36h2f9c1c0_0
hyperlink                 17.3.1                     py_0    conda-forge
icu                       58.2                 h9c2bf20_1
idna                      2.6              py36h82fb2a8_1
imageio                   2.2.0            py36he555465_0
imagesize                 0.7.1            py36h52d8127_0
incremental               17.5.0                     py_0    conda-forge
intel-openmp              2018.0.0             hc7b2577_8
ipykernel                 4.8.0                    py36_0
ipython                   6.2.1            py36h88c514a_1
ipython_genutils          0.2.0            py36hb52b0d5_0
ipywidgets                7.1.1                    py36_0
isort                     4.2.15           py36had401c0_0
itsdangerous              0.24             py36h93cc618_1
jbig                      2.1                  hdba287a_0
jdcal                     1.3              py36h4c697fb_0
jedi                      0.11.1                   py36_0
jinja2                    2.10             py36ha16c418_0
jpeg                      9b                   h024ee3a_2
json-c                    0.12.1                        0    conda-forge
jsonschema                2.6.0            py36h006f8b5_0
jupyter                   1.0.0                    py36_4
jupyter_client            5.2.2                    py36_0
jupyter_console           5.2.0            py36he59e554_1
jupyter_core              4.4.0            py36h7c827e3_0
jupyterlab                0.31.5                   py36_0
jupyterlab_launcher       0.10.2                   py36_0
kealib                    1.4.7                         4    conda-forge
krb5                      1.14.2                        0    conda-forge
lazy-object-proxy         1.3.1            py36h10fcdad_0
libcurl                   7.58.0               h1ad7b7a_0

(...)

Any ideas what may be the problem?

回答1:

I guess this problem comes from conflicts with stuff already installed in the Anaconda distribution. My inelegant workaround is:

conda install -c conda-forge geopandas
conda remove geopandas fiona
pip install geopandas fiona

回答2:

Because I did not wanted to uninstall geopandas, I solved de issue upgrading fiona via pip

pip install --upgrade fiona