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GDAL import error #213

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emthompson-usgs opened this issue Jul 24, 2018 · 1 comment
Closed

GDAL import error #213

emthompson-usgs opened this issue Jul 24, 2018 · 1 comment

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@emthompson-usgs
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Issue:
The following import fails in linux:

In [1]: from osgeo import osr
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-f3ebf498af2a> in <module>()
----> 1 from osgeo import osr

~/miniconda/envs/gf/lib/python3.5/site-packages/osgeo/__init__.py in <module>()
     19                 fp.close()
     20             return _mod
---> 21     _gdal = swig_import_helper()
     22     del swig_import_helper
     23 else:

~/miniconda/envs/gf/lib/python3.5/site-packages/osgeo/__init__.py in swig_import_helper()
     15         if fp is not None:
     16             try:
---> 17                 _mod = imp.load_module('_gdal', fp, pathname, description)
     18             finally:
     19                 fp.close()

~/miniconda/envs/gf/lib/python3.5/imp.py in load_module(name, file, filename, details)
    241                 return load_dynamic(name, filename, opened_file)
    242         else:
--> 243             return load_dynamic(name, filename, file)
    244     elif type_ == PKG_DIRECTORY:
    245         return load_package(name, filename)

~/miniconda/envs/gf/lib/python3.5/imp.py in load_dynamic(name, path, file)
    341         spec = importlib.machinery.ModuleSpec(
    342             name=name, loader=loader, origin=path)
--> 343         return _load(spec)
    344
    345 else:

ImportError: /home/emthompson/miniconda/envs/gf/lib/python3.5/site-packages/osgeo/../../../libgdal.so.20: undefined symbol: _ZN9kmlengine4Href5ParseERKSs

It took a while to identify this as the problem because it does not occur in OSX (same version of gdal), which is what I use for development. It originally showed up as a segmentation fault on Travis CI with pytest. I can provide that info if it would be helpful. The same unit tests with the same install scripts were passing on Travis yesterday.


Environment (conda list): 
$ conda list
# packages in environment at /home/emthompson/miniconda/envs/gf:
#
# Name                    Version                   Build  Channel
affine                    2.2.1                      py_0    conda-forge
alabaster                 0.7.11                     py_3    conda-forge
altair                    2.1.0                      py_0    conda-forge
asn1crypto                0.24.0                     py_1    conda-forge
atomicwrites              1.1.5                    py35_0    conda-forge
attrs                     18.1.0                     py_1    conda-forge
babel                     2.6.0                      py_1    conda-forge
backcall                  0.1.0                      py_0    conda-forge
basemap                   1.1.0                    py35_4    conda-forge
basemap-data-hires        1.1.0                         0    conda-forge
bcrypt                    3.1.4            py35ha35c455_0
beautifulsoup4            4.6.0                    py35_0    conda-forge
blas                      1.0                         mkl
blinker                   1.4                        py_1    conda-forge
blosc                     1.14.0               hfc679d8_1    conda-forge
boost                     1.66.0                   py35_1    conda-forge
boost-cpp                 1.66.0                        1    conda-forge
boto3                     1.7.61                     py_0    conda-forge
botocore                  1.10.61                    py_0    conda-forge
branca                    0.3.0                      py_0    conda-forge
bzip2                     1.0.6                h470a237_2    conda-forge
ca-certificates           2018.4.16                     0    conda-forge
cairo                     1.14.10                       0    conda-forge
cartopy                   0.16.0                   py35_0    conda-forge
certifi                   2018.4.16                py35_0    conda-forge
cffi                      1.11.5                   py35_0    conda-forge
chardet                   3.0.4                    py35_2    conda-forge
click                     6.7                        py_1    conda-forge
click-plugins             1.0.3                      py_1    conda-forge
cligj                     0.4.0                    py35_0    conda-forge
cloudpickle               0.5.3                      py_0    conda-forge
configobj                 5.0.6                    py35_0
coverage                  4.5.1            py35h470a237_1    conda-forge
cryptography              2.3              py35hdffb7b8_0    conda-forge
cryptography-vectors      2.3                      py35_0    conda-forge
curl                      7.60.0                        0    conda-forge
cycler                    0.10.0                     py_1    conda-forge
dask-core                 0.18.2                     py_0    conda-forge
dbus                      1.13.0               h3a4f0e9_0    conda-forge
decorator                 4.3.0                      py_0    conda-forge
descartes                 1.1.0                      py_1    conda-forge
docutils                  0.14                     py35_0    conda-forge
entrypoints               0.2.3                    py35_1    conda-forge
et_xmlfile                1.0.1                    py35_0    conda-forge
expat                     2.2.5                hfc679d8_1    conda-forge
feedgenerator             1.9                        py_1    conda-forge
fiona                     1.7.13                   py35_0    conda-forge
folium                    0.5.0                      py_0    conda-forge
fontconfig                2.12.6                        0    conda-forge
freetype                  2.8.1                         0    conda-forge
freexl                    1.0.5                hf837533_1    conda-forge
future                    0.16.0                   py35_2    conda-forge
gdal                      2.2.4                    py35_0    conda-forge
geos                      3.6.2                hfc679d8_2    conda-forge
geotiff                   1.4.2                hb54a4aa_2    conda-forge
gettext                   0.19.8.1                      0    conda-forge
ghp-import                0.5.5                      py_1    conda-forge
giflib                    5.1.4                h470a237_0    conda-forge
glib                      2.55.0                        0    conda-forge
groundfailure             0.1.dev0                  <pip>
gst-plugins-base          1.8.0                         0    conda-forge
gstreamer                 1.8.0                         1    conda-forge
h5py                      2.8.0            py35h470a237_0    conda-forge
hdf4                      4.2.13                        0    conda-forge
hdf5                      1.10.1                        2    conda-forge
icu                       58.2                 hfc679d8_0    conda-forge
idna                      2.7                      py35_2    conda-forge
imageio                   2.3.0                      py_1    conda-forge
imagesize                 1.0.0                      py_1    conda-forge
impactutils               0.8.6                         1    conda-forge
intel-openmp              2018.0.3                      0
ipython                   6.4.0                    py35_0    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
jdcal                     1.4                        py_1    conda-forge
jedi                      0.12.1                   py35_0    conda-forge
jinja2                    2.10                       py_1    conda-forge
jmespath                  0.9.3                      py_1    conda-forge
jpeg                      9c                   h470a237_0    conda-forge
json-c                    0.12.1                        0    conda-forge
jsonschema                2.6.0                    py35_1    conda-forge
kealib                    1.4.7                         4    conda-forge
kiwisolver                1.0.1                    py35_1    conda-forge
krb5                      1.14.6                        0    conda-forge
libboost                  1.65.1               habcd387_4
libcomcat                 1.2.4                    py35_0    conda-forge
libdap4                   3.18.3                        2    conda-forge
libffi                    3.2.1                         3    conda-forge
libgcc-ng                 7.2.0                hdf63c60_3
libgdal                   2.2.4                         5    conda-forge
libgfortran               3.0.0                         1
libgfortran-ng            7.2.0                hdf63c60_3
libiconv                  1.15                 h470a237_1    conda-forge
libkml                    1.3.0                h9d32c78_3
libnetcdf                 4.6.1                         2    conda-forge
libpng                    1.6.34               ha92aebf_1    conda-forge
libpq                     9.6.3                         0    conda-forge
libspatialite             4.3.0a                       19    conda-forge
libssh2                   1.8.0                h5b517e9_2    conda-forge
libstdcxx-ng              7.2.0                hdf63c60_3
libtiff                   4.0.9                he6b73bb_1    conda-forge
libxcb                    1.13                 h470a237_2    conda-forge
libxml2                   2.9.8                h422b904_2    conda-forge
libxslt                   1.1.32               h88dbc4e_1    conda-forge
lxml                      4.2.3            py35hc9114bc_0    conda-forge
lzo                       2.10                          0    conda-forge
mapio                     0.7.10                     py_0    conda-forge
markdown                  2.6.11                     py_0    conda-forge
markupsafe                1.0                      py35_0    conda-forge
matplotlib                2.2.2                    py35_1    conda-forge
mkl                       2018.0.3                      1
mkl_fft                   1.0.4                    py35_0    conda-forge
mkl_random                1.0.1                    py35_0    conda-forge
more-itertools            4.2.0                    py35_1    conda-forge
munch                     2.3.2                      py_0    conda-forge
ncurses                   5.9                          10    conda-forge
networkx                  2.1                        py_1    conda-forge
nose                      1.3.7                    py35_2    conda-forge
numexpr                   2.6.5                    py35_0    conda-forge
numpy                     1.14.5           py35hcd700cb_0
numpy-base                1.14.5           py35hdbf6ddf_0
obspy                     1.1.0                    py35_1    conda-forge
olefile                   0.45.1                     py_1    conda-forge
openblas                  0.2.20                        8    conda-forge
openjpeg                  2.3.0                h0e734dc_3    conda-forge
openpyxl                  2.5.4                      py_1    conda-forge
openssl                   1.0.2o                        0    conda-forge
owslib                    0.16.0                     py_0    conda-forge
packaging                 17.1                       py_0    conda-forge
pandas                    0.23.3                   py35_0    conda-forge
paramiko                  2.4.1                    py35_0    conda-forge
parso                     0.3.0                      py_0    conda-forge
pcre                      8.41                          1    conda-forge
pelican                   3.7.1                      py_1    conda-forge
pexpect                   4.6.0                    py35_0    conda-forge
pickleshare               0.7.4                    py35_0    conda-forge
pillow                    5.2.0                    py35_0    conda-forge
pip                       18.0                      <pip>
pip                       10.0.1                   py35_0    conda-forge
pixman                    0.34.0                        2    conda-forge
pluggy                    0.6.0                      py_0    conda-forge
pockets                   0.6.2                     <pip>
poppler                   0.61.1                        3    conda-forge
poppler-data              0.4.9                         0    conda-forge
proj4                     4.9.3                         5    conda-forge
prompt_toolkit            1.0.15                   py35_0    conda-forge
pthread-stubs             0.4                  h470a237_1    conda-forge
ptyprocess                0.6.0                    py35_0    conda-forge
py                        1.5.4                      py_0    conda-forge
pyasn1                    0.4.3                      py_0    conda-forge
pycparser                 2.18                       py_1    conda-forge
pycrypto                  2.6.1                    py35_1    conda-forge
pyepsg                    0.3.2                      py_1    conda-forge
pygments                  2.2.0                      py_1    conda-forge
pynacl                    1.1.2                    py35_0    conda-forge
pyopenssl                 18.0.0                   py35_0    conda-forge
pyparsing                 2.2.0                      py_1    conda-forge
pyproj                    1.9.5.1                  py35_0    conda-forge
pyqt                      5.6.0            py35h8210e8a_6    conda-forge
pyshp                     1.2.12                     py_0    conda-forge
pysocks                   1.6.8                    py35_1    conda-forge
pytables                  3.4.4                    py35_8    conda-forge
pytest                    3.6.3                    py35_0    conda-forge
pytest-cov                2.5.1                      py_1    conda-forge
pytest-faulthandler       1.5.0                    py35_0    conda-forge
pytest-mpl                0.9                        py_0    conda-forge
python                    3.5.5                         1    conda-forge
python-dateutil           2.7.3                      py_0    conda-forge
pytz                      2018.5                     py_0    conda-forge
pywavelets                0.5.2                    py35_1    conda-forge
pyyaml                    3.12                     py35_1    conda-forge
qt                        5.6.2                         7    conda-forge
rasterio                  1.0.0            py35h1b5fcde_0    conda-forge
readline                  7.0                           0    conda-forge
requests                  2.19.1                   py35_1    conda-forge
s3transfer                0.1.13                   py35_0    conda-forge
scikit-image              0.14.0           py35hfc679d8_1    conda-forge
scikit-learn              0.19.1           py35hbf1f462_0
scipy                     1.1.0            py35hfc37229_0
setuptools                40.0.0                   py35_0    conda-forge
shapely                   1.6.4            py35h164cb2d_1    conda-forge
simplegeneric             0.8.1                      py_1    conda-forge
sip                       4.18                     py35_1    conda-forge
six                       1.11.0                   py35_1    conda-forge
snowballstemmer           1.2.1                      py_1    conda-forge
snuggs                    1.4.1                      py_1    conda-forge
sphinx                    1.7.5                    py35_0    conda-forge
sphinx-argparse           0.2.2                     <pip>
sphinx-rtd-theme          0.4.0                     <pip>
sphinxcontrib-napoleon    0.6.1                     <pip>
sphinxcontrib-websupport  1.0.1                    py35_0    conda-forge
sqlalchemy                1.2.10                   py35_0    conda-forge
sqlite                    3.20.1                        2    conda-forge
tk                        8.6.8                         0    conda-forge
toolz                     0.9.0                      py_0    conda-forge
tornado                   5.1                      py35_0    conda-forge
traitlets                 4.3.2                    py35_0    conda-forge
typing                    3.6.4                    py35_2    conda-forge
unidecode                 1.0.22                     py_1    conda-forge
urllib3                   1.23                     py35_0    conda-forge
util-linux                2.21                          0
vincent                   0.4.4                      py_1    conda-forge
wcwidth                   0.1.7                      py_1    conda-forge
wheel                     0.31.1                   py35_0    conda-forge
xerces-c                  3.2.0                         0    conda-forge
xlrd                      1.1.0                      py_2    conda-forge
xlsxwriter                1.0.5                      py_0    conda-forge
xlwt                      1.3.0                      py_1    conda-forge
xorg-libxau               1.0.8                h470a237_6    conda-forge
xorg-libxdmcp             1.1.2                h470a237_7    conda-forge
xz                        5.2.3                         0    conda-forge
yaml                      0.1.7                         0    conda-forge
zlib                      1.2.11               h470a237_3    conda-forge

Details about conda and system ( conda info ): 
$ conda info

     active environment : gf
    active env location : /home/emthompson/miniconda/envs/gf
            shell level : 1
       user config file : /home/emthompson/.condarc
 populated config files : /home/emthompson/.condarc
          conda version : 4.5.4
    conda-build version : not installed
         python version : 3.6.5.final.0
       base environment : /home/emthompson/miniconda  (writable)
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/linux-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /home/emthompson/miniconda/pkgs
                          /home/emthompson/.conda/pkgs
       envs directories : /home/emthompson/miniconda/envs
                          /home/emthompson/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.4 requests/2.18.4 CPython/3.6.5 Linux/3.10.0-862.6.3.el7.x86_64 rhel/7.5 glibc/2.17
                UID:GID : 176539137:176539137
             netrc file : None
           offline mode : False
@ocefpaf
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ocefpaf commented Jul 24, 2018

I see a mixture of packages from defaults and conda-forge there. Please take a look at https://conda-forge.org/docs/conda-forge_gotchas.html

To confirm that everything works you can try:

conda create --name GDAL python=3.5 gdal --channel conda-forge --yes
conda activate GDAL
python -c 'from osgeo import osr; print(dir(osr))'

@ocefpaf ocefpaf closed this as completed Jul 24, 2018
@emthompson-usgs emthompson-usgs mentioned this issue Jul 25, 2018
Closed
@ThirstyGeo ThirstyGeo mentioned this issue Dec 12, 2018
Closed
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