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conda-forge / pynio-feedstock

A conda-smithy repository for pynio.
BSD 3-Clause "New" or "Revised" License
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undefined symbol error via libgdal.so.20 #58

Closed pmspire closed 5 years ago

pmspire commented 5 years ago

Issue:

~ % conda create -y -n pynio -c conda-forge --override-channels pynio >out 2>&1
~ % conda activate pynio
(pynio) ~ % python -c 'import Nio'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/pmadden/miniconda/envs/pynio/lib/python3.6/site-packages/PyNIO/Nio.py", line 83, in <module>
    from _nio import *
ImportError: /home/pmadden/miniconda/envs/pynio/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs
(pynio) ~ %


Environment (conda list):

``` (pynio) ~ % conda list # packages in environment at /home/pmadden/miniconda/envs/pynio: # # 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 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 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 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 ncurses 6.1 hf484d3e_1002 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 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 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 ):

``` (pynio) ~ % conda info active environment : pynio active env location : /home/pmadden/miniconda/envs/pynio shell level : 1 user config file : /home/pmadden/.condarc populated config files : conda version : 4.5.12 conda-build version : 3.17.7 python version : 3.7.2.final.0 base environment : /home/pmadden/miniconda (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 : /home/pmadden/miniconda/pkgs /home/pmadden/.conda/pkgs envs directories : /home/pmadden/miniconda/envs /home/pmadden/.conda/envs platform : linux-64 user-agent : conda/4.5.12 requests/2.21.0 CPython/3.7.2 Linux/4.15.0-43-generic ubuntu/18.04 glibc/2.27 UID:GID : 1000:1000 netrc file : /home/pmadden/.netrc offline mode : False ```
ocefpaf commented 5 years ago

Note that pynio was not migrated to the new compilers b/c it depends on hdfeos2 and hdfeos5 and both are still pending due to compilation errors. See https://github.com/conda-forge/hdfeos5-feedstock/pull/22 and https://github.com/conda-forge/hdfeos2-feedstock/pull/18

B/c of that you may need to install the old version compiled with the old compilers. Try:

conda create --name PYNIO --channel conda-forge/label/cf201901 pynio
conda activate PYNIO
python -c 'import Nio'
pmspire commented 5 years ago

Thanks for the workaround, @ocefpaf -- I can confirm that it works for me. Your support is, as always, much appreciated.

ocefpaf commented 5 years ago

Thanks for the workaround, @ocefpaf -- I can confirm that it works for me. Your support is, as always, much appreciated.

Note that as soon as we "fix" hdfeos you can drop that workaround and use the packages with the new compilers. (It may take a while though...)

Leaving this open so other can find it.

jhamman commented 5 years ago

@ocefpaf - we're running into this problem with xarray's ci system too. It looks like the hdfeos issues have been fixed. Does that mean pynio can be rebuilt with the new compilers now?

ocefpaf commented 5 years ago

@ocefpaf - we're running into this problem with xarray's ci system too. It looks like the hdfeos issues have been fixed. Does that mean pynio can be rebuilt with the new compilers now?

Let me check, maybe there are other package that are missing. (The PR should happen automatically so we are either missing a package or the bot is nor working properly.)

ocefpaf commented 5 years ago

Found the missing package, it was g2clib, a PR to pynio should follow soon.

xiang-yu commented 5 years ago

I still got the same error even following the procedures below,

$ conda create --name PYNIO --channel conda-forge/label/cf201901 pynio $ conda activate PYNIO $ python -c 'import Nio'

$ ipython In [1]: import Nio

ImportError Traceback (most recent call last)

in ----> 1 import Nio ~/anaconda3/lib/python3.6/site-packages/PyNIO/Nio.py in 81 ''' 82 from __future__ import print_function ---> 83 from _nio import * 84 85 # ImportError: /home/xyli/anaconda3/lib/python3.6/site-packages/PyNIO/../../../libgdal.so.20: undefined symbol: _ZN6libdap3DDSC1EPNS_15BaseTypeFactoryERKSs Any idea about how to fix this?
ocefpaf commented 5 years ago

I believe that the compilation of pynio with the new compilers is done. First ensure that you have conda-forge on top of defaults in your .condarc and activate the strict channel option:

conda config --set channel_priority strict
conda config --add channels conda-forge

then do,

conda create --name PYNIO --channel conda-forge pynio
conda activate PYNIO
python -c 'import Nio'
xiang-yu commented 5 years ago

Thanks a lot.

I got the following error after $ python -c 'import Nio' ImportError: libnsl.so.1: cannot open shared object file: No such file or directory

ocefpaf commented 5 years ago

Can you post the conda list of that env? The command did work for me.

xiang-yu commented 5 years ago

$ conda list PYNIO

packages in environment at /home/xyli/anaconda3:

#

Name Version Build Channel

pynio 1.5.4 py36h36f4ed2_0 conda-forge/label/cf201901

ocefpaf commented 5 years ago

pynio 1.5.4 py36h36f4ed2_0 conda-forge/label/cf201901

That is still the package from the cf201901 label. Like I said above the compilation problems that forced us to use that label are gone.

Can you try the commands in https://github.com/conda-forge/pynio-feedstock/issues/58#issuecomment-472958526 and install it from the main label instead.

xiang-yu commented 5 years ago

$ conda create --name PYNIO --channel conda-forge pynio $ conda activate PYNIO $ python -c 'import Nio' Traceback (most recent call last): File "", line 1, in File "/home/xyli/anaconda3/envs/PYNIO/lib/python3.7/site-packages/PyNIO/Nio.py", line 83, in from _nio import * ImportError: libnsl.so.1: cannot open shared object file: No such file or directory

$ conda list PYNIO

packages in environment at /home/xyli/anaconda3/envs/PYNIO:

#

Name Version Build Channel

pynio 1.5.5 py37h8b983ae_0 conda-forge

ocefpaf commented 5 years ago

Did you do the first two steps?

xiang-yu commented 5 years ago

Thanks. Yes. $ conda config --set channel_priority strict $ conda config --add channels conda-forge

ocefpaf commented 5 years ago

I cannot reproduce that error locally. It would be helpful if you list all the files in conda list instead of just pynio.

ycherrq commented 5 years ago

Note that pynio was not migrated to the new compilers b/c it depends on hdfeos2 and hdfeos5 and both are still pending due to compilation errors. See conda-forge/hdfeos5-feedstock#22 and conda-forge/hdfeos2-feedstock#18

B/c of that you may need to install the old version compiled with the old compilers. Try:

conda create --name PYNIO --channel conda-forge/label/cf201901 pynio
conda activate PYNIO
python -c 'import Nio'