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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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cannot open shared object file when importing Nio #82

Closed pmspire closed 4 years ago

pmspire commented 4 years ago

Issue:

% conda create -y -c conda-forge -n pynio pynio=1.5.5
...
% conda activate pynio
% python
...
>>> import Nio
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/users/PYS0343/pmadden/.conda/envs/pynio/lib/python3.8/site-packages/PyNIO/Nio.py", line 83, in <module>
    from _nio import *
ImportError: libnetcdf.so.15: cannot open shared object file: No such file or directory

Maybe an upstream issue due to one of the HDF dependencies? If I force libnetcdf=4.6.2, there's no problem.
Environment (conda list):

% conda list # packages in environment at /users/PYS0343/pmadden/.conda/envs/pynio: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge boost-cpp 1.72.0 h8e57a91_0 conda-forge bzip2 1.0.8 h516909a_2 conda-forge ca-certificates 2019.11.28 hecc5488_0 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge certifi 2019.11.28 py38h32f6830_1 conda-forge cfitsio 3.470 hb60a0a2_2 conda-forge curl 7.68.0 hf8cf82a_0 conda-forge expat 2.2.9 he1b5a44_2 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge freetype 2.10.1 he06d7ca_0 conda-forge freexl 1.0.5 h14c3975_1002 conda-forge g2clib 1.6.0 hf3f1b0b_9 conda-forge geos 3.8.1 he1b5a44_0 conda-forge geotiff 1.5.1 hcbe54f9_9 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge giflib 5.2.1 h516909a_2 conda-forge glib 2.58.3 py38h73cb85d_1003 conda-forge hdf4 4.2.13 hf30be14_1003 conda-forge hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge hdfeos2 2.20 h64bfcee_1000 conda-forge hdfeos5 5.1.16 h8b6279f_5 conda-forge icu 64.2 he1b5a44_1 conda-forge jasper 1.900.1 h07fcdf6_1006 conda-forge jpeg 9c h14c3975_1001 conda-forge json-c 0.13.1 h14c3975_1001 conda-forge kealib 1.4.12 hec59c27_0 conda-forge krb5 1.16.4 h2fd8d38_0 conda-forge ld_impl_linux-64 2.34 h53a641e_0 conda-forge libblas 3.8.0 16_openblas conda-forge libcblas 3.8.0 16_openblas conda-forge libcurl 7.68.0 hda55be3_0 conda-forge libdap4 3.20.4 hd3bb157_0 conda-forge libedit 3.1.20170329 hf8c457e_1001 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgdal 3.0.4 hce44138_2 conda-forge libgfortran-ng 7.3.0 hdf63c60_5 conda-forge libiconv 1.15 h516909a_1006 conda-forge libkml 1.3.0 hb574062_1011 conda-forge liblapack 3.8.0 16_openblas conda-forge libnetcdf 4.7.4 nompi_h9f9fd6a_100 conda-forge libopenblas 0.3.9 h5ec1e0e_0 conda-forge libpng 1.6.37 hed695b0_1 conda-forge libpq 12.2 hae5116b_0 conda-forge libspatialite 4.3.0a heb269f5_1037 conda-forge libssh2 1.8.2 h22169c7_2 conda-forge libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge libtiff 4.1.0 hc3755c2_3 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libwebp 1.0.2 h56121f0_5 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.10 hee79883_0 conda-forge llvm-openmp 9.0.1 hc9558a2_2 conda-forge lz4-c 1.8.3 he1b5a44_1001 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.18.1 py38h8854b6b_1 conda-forge openjpeg 2.3.1 h981e76c_3 conda-forge openssl 1.1.1e h516909a_0 conda-forge pcre 8.44 he1b5a44_0 conda-forge pip 20.0.2 py_2 conda-forge pixman 0.38.0 h516909a_1003 conda-forge poppler 0.67.0 h14e79db_8 conda-forge poppler-data 0.4.9 1 conda-forge postgresql 12.2 hf1211e9_0 conda-forge proj 6.3.1 hc80f0dc_1 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge pynio 1.5.5 py38hb7a502c_10 conda-forge python 3.8.2 h8356626_5_cpython conda-forge python_abi 3.8 1_cp38 conda-forge readline 8.0 hf8c457e_0 conda-forge setuptools 46.1.3 py38h32f6830_0 conda-forge sqlite 3.30.1 hcee41ef_0 conda-forge tbb 2018.0.5 h2d50403_0 conda-forge tiledb 1.7.0 hcde45ca_2 conda-forge tk 8.6.10 hed695b0_0 conda-forge tzcode 2019a h516909a_1002 conda-forge wheel 0.34.2 py_1 conda-forge xerces-c 3.2.2 h8412b87_1004 conda-forge xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.9 h516909a_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_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 h516909a_1002 conda-forge zlib 1.2.11 h516909a_1006 conda-forge zstd 1.4.4 h3b9ef0a_2 conda-forge


Details about conda and system ( conda info ):

``` % conda info active environment : pynio active env location : /users/PYS0343/pmadden/.conda/envs/pynio shell level : 2 user config file : /users/PYS0343/pmadden/.condarc populated config files : conda version : 4.8.2 conda-build version : 3.18.11 python version : 3.7.6.final.0 virtual packages : __glibc=2.17 base environment : /users/PYS0343/wxops/sw/conda (read only) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /users/PYS0343/pmadden/.conda/pkgs envs directories : /users/PYS0343/pmadden/.conda/envs /users/PYS0343/wxops/sw/conda/envs platform : linux-64 user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Linux/3.10.0-957.41.1.el7.x86_64 rhel/7.6 glibc/2.17 UID:GID : 30065:5387 netrc file : /users/PYS0343/pmadden/.netrc offline mode : False ```
ocefpaf commented 4 years ago

Latest libnetcdf broke backwards compatibility. I just removed that package and this should be solved soon.