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basemap + gdal: libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs #43

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danschef opened this issue Jan 18, 2019 · 4 comments
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basemap + gdal: libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs #43

danschef opened this issue Jan 18, 2019 · 4 comments

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@danschef
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danschef commented Jan 18, 2019 •
edited

Dear all,

I just ran into an error when installing basemap and gdal within the same Anaconda environment like this:

conda create -n test gdal basemap -c conda-forge

The basemap import works fine but when I try to import gdal, I get this:

Python 3.6.7 | packaged by conda-forge | (default, Nov 21 2018, 03:09:43)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import gdal
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/root/miniconda3/envs/test/lib/python3.6/site-packages/osgeo/__init__.py", line 21, in <module>
    _gdal = swig_import_helper()
  File "/root/miniconda3/envs/test/lib/python3.6/site-packages/osgeo/__init__.py", line 17, in swig_import_helper
    _mod = imp.load_module('_gdal', fp, pathname, description)
  File "/root/miniconda3/envs/test/lib/python3.6/imp.py", line 243, in load_module
    return load_dynamic(name, filename, file)
  File "/root/miniconda3/envs/test/lib/python3.6/imp.py", line 343, in load_dynamic
    return _load(spec)
ImportError: /root/miniconda3/envs/test/lib/python3.6/site-packages/osgeo/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs

Environment (conda list): 
(test) [root@df11cf60d6c3 ~]# conda list
# packages in environment at /root/miniconda3/envs/test:
#
# Name                    Version                   Build  Channel
basemap                   1.2.0           py36hb9db7be_1000    conda-forge
blas                      1.0                         mkl
boost-cpp                 1.68.0            h11c811c_1000    conda-forge
bzip2                     1.0.6             h14c3975_1002    conda-forge
ca-certificates           2018.11.29           ha4d7672_0    conda-forge
cairo                     1.14.12           h80bd089_1005    conda-forge
certifi                   2018.11.29            py36_1000    conda-forge
curl                      7.63.0            h646f8bb_1000    conda-forge
cycler                    0.10.0                     py_1    conda-forge
dbus                      1.13.0            h4e0c4b3_1000    conda-forge
expat                     2.2.5             hf484d3e_1002    conda-forge
fontconfig                2.13.1            h2176d3f_1000    conda-forge
freetype                  2.9.1             h3cfcefd_1004    conda-forge
freexl                    1.0.5             h14c3975_1002    conda-forge
gdal                      2.3.2            py36hb00a9d7_0    conda-forge
geos                      3.6.2                hfc679d8_4    conda-forge
geotiff                   1.4.2             hfe6da40_1005    conda-forge
gettext                   0.19.8.1          h9745a5d_1001    conda-forge
giflib                    5.1.4             h14c3975_1001    conda-forge
glib                      2.56.2            had28632_1001    conda-forge
gst-plugins-base          1.12.5            h3865690_1000    conda-forge
gstreamer                 1.12.5            h0cc0488_1000    conda-forge
hdf4                      4.2.13            h9a582f1_1002    conda-forge
hdf5                      1.10.3            hba1933b_1001    conda-forge
icu                       58.2              hf484d3e_1000    conda-forge
intel-openmp              2019.1                      144
jpeg                      9c                h14c3975_1001    conda-forge
json-c                    0.12.1               h470a237_1    conda-forge
kealib                    1.4.10            hc069b17_1000    conda-forge
kiwisolver                1.0.1           py36h6bb024c_1002    conda-forge
krb5                      1.16.3            hc83ff2d_1000    conda-forge
libcurl                   7.63.0            h01ee5af_1000    conda-forge
libdap4                   3.19.1            hd48c02d_1000    conda-forge
libedit                   3.1.20170329      hf8c457e_1001    conda-forge
libffi                    3.2.1             hf484d3e_1005    conda-forge
libgcc-ng                 7.3.0                hdf63c60_0    conda-forge
libgdal                   2.3.2                hc73897a_0    conda-forge
libgfortran-ng            7.2.0                hdf63c60_3    conda-forge
libiconv                  1.15              h14c3975_1004    conda-forge
libkml                    1.3.0             h328b03d_1009    conda-forge
libnetcdf                 4.6.1             hc6a9f4b_1010    conda-forge
libpng                    1.6.36            h84994c4_1000    conda-forge
libpq                     10.6              h13b8bad_1000    conda-forge
libspatialite             4.3.0a            h9968ff2_1023    conda-forge
libssh2                   1.8.0             h1ad7b7a_1003    conda-forge
libstdcxx-ng              7.3.0                hdf63c60_0    conda-forge
libtiff                   4.0.10            h648cc4a_1001    conda-forge
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.13              h14c3975_1002    conda-forge
libxml2                   2.9.8             h143f9aa_1005    conda-forge
matplotlib                3.0.2           py36h8a2030e_1001    conda-forge
matplotlib-base           3.0.2           py36h167e16e_1001    conda-forge
mkl                       2019.1                      144
mkl_fft                   1.0.10           py36h470a237_1    conda-forge
mkl_random                1.0.2                    py36_0    conda-forge
ncurses                   6.1               hf484d3e_1002    conda-forge
numpy                     1.15.4           py36h7e9f1db_0
numpy-base                1.15.4           py36hde5b4d6_0
openjpeg                  2.3.0             hf38bd82_1003    conda-forge
openssl                   1.0.2p            h14c3975_1002    conda-forge
pcre                      8.41              hf484d3e_1003    conda-forge
pip                       18.1                  py36_1000    conda-forge
pixman                    0.34.0            h14c3975_1003    conda-forge
poppler                   0.67.0            h2fc8fa2_1002    conda-forge
poppler-data              0.4.9                         1    conda-forge
postgresql                10.6              h66cca7a_1000    conda-forge
proj4                     4.9.3                h470a237_8    conda-forge
pthread-stubs             0.4               h14c3975_1001    conda-forge
pyparsing                 2.3.1                      py_0    conda-forge
pyproj                    1.9.5.1         py36h2944ce7_1006    conda-forge
pyqt                      5.6.0           py36h13b7fb3_1008    conda-forge
pyshp                     2.0.1                      py_0    conda-forge
python                    3.6.7             hd21baee_1001    conda-forge
python-dateutil           2.7.5                      py_0    conda-forge
qt                        5.6.2                hf70d934_9    conda-forge
readline                  7.0               hf8c457e_1001    conda-forge
setuptools                40.6.3                   py36_0    conda-forge
sip                       4.18.1          py36hf484d3e_1000    conda-forge
six                       1.12.0                py36_1000    conda-forge
sqlite                    3.26.0            h67949de_1000    conda-forge
tk                        8.6.9             h84994c4_1000    conda-forge
tornado                   5.1.1           py36h14c3975_1000    conda-forge
tzcode                    2018g             h14c3975_1001    conda-forge
wheel                     0.32.3                   py36_0    conda-forge
xerces-c                  3.2.0                h5d6a6da_2    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.9             h14c3975_1004    conda-forge
xorg-libsm                1.2.3             h4937e3b_1000    conda-forge
xorg-libx11               1.6.6             h14c3975_1000    conda-forge
xorg-libxau               1.0.8             h14c3975_1006    conda-forge
xorg-libxdmcp             1.1.2             h14c3975_1007    conda-forge
xorg-libxext              1.3.3             h14c3975_1004    conda-forge
xorg-libxrender           0.9.10            h14c3975_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.4             h14c3975_1001    conda-forge
zlib                      1.2.11            h14c3975_1004    conda-forge

Details about conda and system ( conda info ): 
(test) [root@df11cf60d6c3 ~]# conda info

     active environment : test
    active env location : /root/miniconda3/envs/test
            shell level : 2
       user config file : /root/.condarc
 populated config files :
          conda version : 4.5.12
    conda-build version : not installed
         python version : 3.7.1.final.0
       base environment : /root/miniconda3  (writable)
           channel URLs : 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 : /root/miniconda3/pkgs
                          /root/.conda/pkgs
       envs directories : /root/miniconda3/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.12 requests/2.21.0 CPython/3.7.1 Linux/3.13.0-119-generic centos/7 glibc/2.17
                UID:GID : 0:0
             netrc file : None
           offline mode : False

Any suggestions?

EDIT:
I just found out that I can avoid the error by pinning geos to >3.7.0. This downgrades basemap to 1.0.8.dev0. So one of the following works for me:

conda create -n test gdal basemap "geos>3.7.0" -c conda-forge
or
conda create -n test gdal "basemap=1.0.8.dev0" -c conda-forge
@ocefpaf ocefpaf mentioned this issue Jan 18, 2019
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@mariusvniekerk
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@conda-forge-admin please rerender

@conda-forge-linter conda-forge-linter mentioned this issue Jan 20, 2019
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@conda-forge-linter
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Hi! This is the friendly automated conda-forge-webservice.

I just wanted to let you know that I rerendered the recipe in #44.

@ocefpaf ocefpaf closed this as completed Jan 21, 2019
@danschef
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Thanks for the fix!

@dnivrav
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dnivrav commented Feb 16, 2019

pinning geos to >3.7.0 gives me the following error:

CondaValueError: prefix already exists: /home/arvind/anaconda3/envs/test

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@mariusvniekerk @ocefpaf @danschef @conda-forge-linter @dnivrav