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conda-forge / netcdf4-feedstock

A conda-smithy repository for netcdf4.
BSD 3-Clause "New" or "Revised" License
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Import failure due to libssh2 issue #88

Closed djgagne closed 5 years ago

djgagne commented 5 years ago

Issue: When importing netCDF4, I ran into the following error:

>>> from netCDF4 import Dataset
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/dgagne/miniconda3/envs/ml/lib/python3.6/site-packages/netCDF4/__init__.py", line 3, in <module>
    from ._netCDF4 import *
ImportError: dlopen(/Users/dgagne/miniconda3/envs/ml/lib/python3.6/site-packages/netCDF4/_netCDF4.cpython-36m-darwin.so, 2): Library not loaded: @rpath/libssl.1.0.0.dylib
  Referenced from: /Users/dgagne/miniconda3/envs/ml/lib/libssh2.1.dylib
  Reason: image not found

I was able to fix the problem by manually updating libssh2 from 1.8.0-1 to 1.8.2-hcdc9a53_2. However, updating netcdf with conda update netcdf4 only upgraded the netcdf4 binary but not the libssh2 binary. Is there a way to fix the dependencies to make sure libssh2 also updates when updating netcdf4? I am currently running on macOS 10.13.6 (High Sierra).
Environment (conda list):

``` $ conda list # packages in environment at /Users/dgagne/miniconda3/envs/ml: # # Name Version Build Channel absl-py 0.7.0 pypi_0 pypi alabaster 0.7.12 py_0 conda-forge ams-ml-python-course 0.1 dev_0 appnope 0.1.0 py36_1000 conda-forge astor 0.7.1 pypi_0 pypi atomicwrites 1.3.0 py_0 conda-forge attrs 19.1.0 pypi_0 pypi babel 2.6.0 py_1 conda-forge backcall 0.1.0 py_0 conda-forge blas 2.5 openblas conda-forge bleach 3.1.0 py_0 conda-forge blosc 1.15.1 h0a44026_1002 conda-forge bokeh 1.0.4 py36_1000 conda-forge bzip2 1.0.6 h1de35cc_1002 conda-forge ca-certificates 2019.3.9 hecc5488_0 conda-forge cartopy 0.17.0 py36h929c6f0_1004 conda-forge certifi 2019.3.9 py36_0 conda-forge cftime 1.0.3.4 py36h917ab60_1000 conda-forge click 7.0 py_0 conda-forge cloudpickle 0.7.0 py_0 conda-forge curl 7.64.0 heae2a1f_2 conda-forge cycler 0.10.0 pypi_0 pypi cytoolz 0.9.0.1 py36h1de35cc_1001 conda-forge dask 1.1.4 py_0 conda-forge dask-core 1.1.4 py_0 conda-forge decorator 4.3.2 py_0 conda-forge distributed 1.26.0 py36_1 conda-forge docutils 0.14 py36_1001 conda-forge entrypoints 0.3 py36_1000 conda-forge ephem 3.7.6.0 py36h1de35cc_1001 conda-forge freetype 2.9.1 h597ad8a_1005 conda-forge gast 0.2.2 pypi_0 pypi geos 3.7.1 h0a44026_1000 conda-forge grpcio 1.18.0 pypi_0 pypi h5py 2.9.0 pypi_0 pypi hdf4 4.2.13 hf3c6af0_1002 conda-forge hdf5 1.10.4 nompi_h646315f_1105 conda-forge heapdict 1.0.0 py36_1000 conda-forge icu 58.2 h0a44026_1000 conda-forge imagesize 1.1.0 py_0 conda-forge ipykernel 5.1.0 py36h24bf2e0_1002 conda-forge ipython 7.2.0 py36h24bf2e0_1000 conda-forge ipython-genutils 0.2.0 pypi_0 pypi ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.4.2 py_0 conda-forge jedi 0.13.2 py36_1000 conda-forge jinja2 2.10 pypi_0 pypi jpeg 9c h1de35cc_1001 conda-forge jsonschema 3.0.0a3 py36_1000 conda-forge jupyter 1.0.0 py_1 conda-forge jupyter-console 6.0.0 pypi_0 pypi jupyter_client 5.2.4 py_1 conda-forge jupyter_console 6.0.0 py_0 conda-forge jupyter_core 4.4.0 py_0 conda-forge jupyterlab 0.35.4 py36_0 conda-forge jupyterlab_server 0.2.0 py_0 conda-forge keras 2.2.4 pypi_0 pypi keras-applications 1.0.7 pypi_0 pypi keras-preprocessing 1.0.9 pypi_0 pypi kiwisolver 1.0.1 py36h04f5b5a_1002 conda-forge krb5 1.16.3 hcfa6398_1001 conda-forge libblas 3.8.0 5_openblas conda-forge libcblas 3.8.0 5_openblas conda-forge libcurl 7.64.0 he376013_2 conda-forge libcxx 7.0.0 h2d50403_2 conda-forge libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 h0a44026_1005 conda-forge libgfortran 3.0.1 0 conda-forge libiconv 1.15 h1de35cc_1004 conda-forge liblapack 3.8.0 5_openblas conda-forge liblapacke 3.8.0 5_openblas conda-forge libnetcdf 4.6.2 h6b88ef6_1001 conda-forge libpng 1.6.36 ha441bb4_1000 conda-forge libsodium 1.0.16 h1de35cc_1001 conda-forge libssh2 1.8.0 1 conda-forge libtiff 4.0.10 h79f4b77_1001 conda-forge libxml2 2.9.8 hf14e9c8_1005 conda-forge libxslt 1.1.32 h33a18ac_1002 conda-forge llvm-meta 7.0.0 0 conda-forge llvmlite 0.26.0 py36h3fea490_1000 conda-forge locket 0.2.0 py_2 conda-forge lorenz-gan 0.1 dev_0 lxml 4.3.1 py36h7166777_0 conda-forge markdown 3.0.1 pypi_0 pypi markupsafe 1.1.0 py36h1de35cc_1000 conda-forge matplotlib 3.0.2 py36_1002 conda-forge matplotlib-base 3.0.2 py36hf043ca5_1002 conda-forge mistune 0.8.4 py36h1de35cc_1000 conda-forge mlmicrophysics 0.1 dev_0 mlsurfacelayer 0.1 dev_0 mock 2.0.0 pypi_0 pypi more-itertools 4.3.0 py36_1000 conda-forge msgpack-python 0.6.1 py36h04f5b5a_0 conda-forge nbconvert 5.3.1 py_1 conda-forge nbformat 4.4.0 py_1 conda-forge ncurses 6.1 h0a44026_1002 conda-forge netcdf-fortran 4.4.5 h5ce9b53_1000 conda-forge netcdf4 1.5.1.2 py36h58b02fa_0 conda-forge notebook 5.7.4 py36_1000 conda-forge numba 0.41.0 py36h1702cab_1000 conda-forge numexpr 2.6.9 py36h1702cab_1000 conda-forge numpy 1.16.3 py36hdf140aa_0 conda-forge olefile 0.46 py_0 conda-forge openblas 0.3.5 h436c29b_1001 conda-forge openssl 1.1.1b h01d97ff_2 conda-forge owslib 0.17.1 py_0 conda-forge packaging 19.0 py_0 conda-forge pandas 0.24.1 py36h0a44026_0 conda-forge pandoc 2.6 1 conda-forge pandocfilters 1.4.2 py_1 conda-forge parso 0.3.4 py_0 conda-forge partd 0.3.9 py_0 conda-forge pbr 5.1.3 pypi_0 pypi pexpect 4.6.0 py36_1000 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 5.4.1 py36hbddbef0_1000 conda-forge pip 19.0.2 py36_0 conda-forge pluggy 0.11.0 py_0 conda-forge proj4 5.2.0 h1de35cc_1001 conda-forge prometheus_client 0.5.0 py_0 conda-forge prompt_toolkit 2.0.8 py_0 conda-forge protobuf 3.6.1 pypi_0 pypi psutil 5.5.0 py36h1de35cc_0 conda-forge ptyprocess 0.6.0 py36_1000 conda-forge pvlib-python 0.6.1 py_0 conda-forge py 1.8.0 py_0 conda-forge pyepsg 0.4.0 py_0 conda-forge pygments 2.3.1 py_0 conda-forge pykdtree 1.3.1 py36h917ab60_1002 conda-forge pyparsing 2.3.1 py_0 conda-forge pyproj 1.9.6 py36h9c430a6_1000 conda-forge pyqt 5.6.0 py36hc26a216_1008 conda-forge pyrsistent 0.14.10 py36h1de35cc_0 conda-forge pyshp 2.0.1 py_0 conda-forge pytables 3.4.4 py36h0af8b44_1004 conda-forge pytest 4.4.2 py36_0 conda-forge python 3.6.7 h8dc6b48_1004 conda-forge python-dateutil 2.8.0 py_0 conda-forge pytz 2018.9 py_0 conda-forge pyyaml 3.13 py36h1de35cc_1001 conda-forge pyzmq 17.1.2 py36h111632d_1001 conda-forge qt 5.6.2 h822fa55_1013 conda-forge qtconsole 4.4.3 pypi_0 pypi readline 7.0 hcfe32e1_1001 conda-forge requests 2.13.0 py36_0 conda-forge scikit-learn 0.20.2 py36_blas_openblashc6dc708_1400 [blas_openblas] conda-forge scipy 1.2.0 py36_blas_openblash486cb9f_1201 [blas_openblas] conda-forge send2trash 1.5.0 py_0 conda-forge setuptools 40.8.0 py36_0 conda-forge shapely 1.6.4 py36h2bcc7ef_1002 conda-forge sip 4.18.1 py36h0a44026_1000 conda-forge six 1.12.0 py36_1000 conda-forge snowballstemmer 1.2.1 py_1 conda-forge sortedcontainers 2.1.0 py_0 conda-forge sphinx 1.8.4 py36_0 conda-forge sphinxcontrib-websupport 1.1.0 py_1 conda-forge sqlite 3.26.0 h1765d9f_1000 conda-forge tblib 1.3.2 py_1 conda-forge tensorboard 1.13.1 pypi_0 pypi tensorflow 1.13.1 pypi_0 pypi tensorflow-estimator 1.13.0 pypi_0 pypi tensorflow-probability 0.6.0 pypi_0 pypi termcolor 1.1.0 pypi_0 pypi terminado 0.8.1 py36_1001 conda-forge testpath 0.4.2 py36_1000 conda-forge tk 8.6.9 ha441bb4_1000 conda-forge toolz 0.9.0 py_1 conda-forge tornado 5.1.1 py36h1de35cc_1000 conda-forge traitlets 4.3.2 py36_1000 conda-forge wcwidth 0.1.7 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi werkzeug 0.14.1 pypi_0 pypi wheel 0.33.0 py36_0 conda-forge widgetsnbextension 3.4.2 py36_1000 conda-forge xarray 0.11.3 py36_0 conda-forge xz 5.2.4 h1de35cc_1001 conda-forge yaml 0.1.7 h1de35cc_1001 conda-forge zeromq 4.2.5 h0a44026_1006 conda-forge zict 0.1.3 py_0 conda-forge zlib 1.2.11 h1de35cc_1004 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active environment : ml active env location : /Users/dgagne/miniconda3/envs/ml shell level : 1 user config file : /Users/dgagne/.condarc populated config files : /Users/dgagne/.condarc /Users/dgagne/miniconda3/envs/ml/.condarc conda version : 4.6.3 conda-build version : not installed python version : 3.6.8.final.0 base environment : /Users/dgagne/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch package cache : /Users/dgagne/miniconda3/pkgs /Users/dgagne/.conda/pkgs envs directories : /Users/dgagne/miniconda3/envs /Users/dgagne/.conda/envs platform : osx-64 user-agent : conda/4.6.3 requests/2.18.4 CPython/3.6.8 Darwin/17.7.0 OSX/10.13.6 UID:GID : 493664989:1202617992 netrc file : None offline mode : False ```
ocefpaf commented 5 years ago

It is really odd you got such an old libssh2 package (pre conda-build 3 b/c of the absence of the hash build number). Probably a package with bad metadata. Removed those from main and hopefully that should fix your problem.