libgdal undefined symbol

[havenerk]

Just installed pynio/pyngl via conda, then activated (used conda activate instead of source activate, but should be the same)

Ubuntu Linux: Linux gose 4.18.0-13-generic #14-Ubuntu SMP Wed Dec 5 09:04:24 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

conda create --name pyn_env --channel conda-forge pynio pyngl
source activate pyn_env

Then:
(pyn_env) havenerk@gose:~$ python
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 Nio
Traceback (most recent call last):
File "", line 1, in
File "/home/havenerk/miniconda3/envs/pyn_env/lib/python3.6/site-packages/PyNIO/Nio.py", line 83, in
from _nio import *
ImportError: /home/havenerk/miniconda3/envs/pyn_env/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs

What do I do now? Seems to be a conda/gdal issue, and the internet is all over the place about how to work around it.

Conda list reveals:

pyn_env) havenerk@gose:~$ conda list

packages in environment at /home/havenerk/miniconda3/envs/pyn_env:

Name Version Build Channel

blas 1.1 openblas conda-forge
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
esmf 7.1.0r ha678704_2 conda-forge
expat 2.2.5 hf484d3e_1002 conda-forge
fontconfig 2.13.1 h2176d3f_1000 conda-forge
freetype 2.9.1 h94bbf69_1005 conda-forge
freexl 1.0.5 h14c3975_1002 conda-forge
g2clib 1.6.0 3 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
gsl 2.2.1 blas_openblashddceaf2_6 [blas_openblas] conda-forge
hdf4 4.2.13 h9a582f1_1002 conda-forge
hdf5 1.10.2 hc401514_3 conda-forge
hdfeos2 2.20 h7a90ae3_0 conda-forge
hdfeos5 5.1.16 h647bee3_2 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
jasper 1.900.1 h07fcdf6_1005 conda-forge
jpeg 9c h14c3975_1001 conda-forge
json-c 0.12.1 h470a237_1 conda-forge
kealib 1.4.9 h0bee7d0_2 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 2.2.4 hbd6f514_9 conda-forge
libgfortran 3.0.0 1 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 h628ed10_200 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
mpi 1.0 mpich conda-forge
mpich 3.2.1 h1c2f66e_1007 conda-forge
ncl 6.5.0 blas_openblashd40de8d_1 [blas_openblas] conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf-fortran 4.4.4 h4363f12_9 conda-forge
numpy 1.16.0 py36_blas_openblash1522bff_1000 [blas_openblas] conda-forge
openblas 0.3.3 h9ac9557_1001 conda-forge
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
pyngl 1.6.1 py36h4217dbb_0 conda-forge
pynio 1.5.4 py36h36f4ed2_0 conda-forge
python 3.6.7 hd21baee_1001 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
setuptools 40.6.3 py36_0 conda-forge
sqlite 3.26.0 h67949de_1000 conda-forge
tk 8.6.9 h84994c4_1000 conda-forge
tzcode 2018g h14c3975_1001 conda-forge
udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge
wheel 0.32.3 py36_0 conda-forge
xerces-c 3.2.0 h5d6a6da_2 conda-forge
xorg-imake 1.0.7 0 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-libxaw 1.0.13 h14c3975_1002 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xorg-libxext 1.3.3 h14c3975_1004 conda-forge
xorg-libxmu 1.1.2 h14c3975_1002 conda-forge
xorg-libxpm 3.5.12 h14c3975_1002 conda-forge
xorg-libxrender 0.9.10 h14c3975_1002 conda-forge
xorg-libxt 1.1.5 h14c3975_1002 conda-forge
xorg-makedepend 1.0.5 0 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

[khallock]

Hi @havenerk,

The current workaround is to use the "cf201901" label on the conda-forge channel:
conda create --name pyn_env --channel conda-forge/label/cf201901 pynio pyngl

The conda-forge project migrated to new compilers recently, and PyNIO/PyNGL are holdover packages that have not been built with the new compiler yet (the issue is actually with hdfeos2 and hdfeos5, which are dependencies of PyNIO). See conda-forge/pynio-feedstock#58 for more info.