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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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Error: Library not loaded: @rpath/libssl.1.0.0.dylib #877 #73

Closed johnwoodill closed 5 years ago

johnwoodill commented 5 years ago

Issue: I am receiving the following error when trying to load the package.

import netCDF4 as nc

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


Environment (conda list):

``` $ conda list ``` # Name Version Build Channel _r-mutex 1.0.0 anacondar_1 absl-py 0.7.0 py36_1000 conda-forge alabaster 0.7.12 py_0 conda-forge appdirs 1.4.3 py_1 conda-forge appnope 0.1.0 py36_1000 conda-forge asn1crypto 0.24.0 py36_1003 conda-forge astor 0.7.1 py_0 conda-forge astroid 1.6.4 pypi_0 pypi attrs 18.2.0 py_0 conda-forge automat 0.7.0 py_1 conda-forge babel 2.6.0 py_1 conda-forge backcall 0.1.0 py_0 conda-forge basemap 1.2.0 py36h3f464f3_1001 conda-forge blas 1.0 mkl bleach 3.1.0 py_0 conda-forge bottleneck 1.2.1 pypi_0 pypi brewer2mpl 1.4.1 pypi_0 pypi bwidget 1.9.11 1 bzip2 1.0.6 h1de35cc_1002 conda-forge c-ares 1.15.0 h1de35cc_1001 conda-forge ca-certificates 2018.11.29 ha4d7672_0 conda-forge cachecontrol 0.12.5 pypi_0 pypi cairo 1.14.12 h9d4d9ac_1005 conda-forge cartopy 0.17.0 py36h929c6f0_1004 conda-forge cctools 895 h7512d6f_0 conda-forge cement 2.10.2 pypi_0 pypi certifi 2018.11.29 py36_1000 conda-forge cffi 1.11.5 py36h342bebf_1001 conda-forge cftime 1.0.3.4 py36h917ab60_1000 conda-forge chardet 3.0.4 py36_1003 conda-forge clang 4.0.1 h662ec87_0 conda-forge clang_osx-64 4.0.1 h1ce6c1d_11 conda-forge clangxx 4.0.1 hc9b4283_0 clangxx_osx-64 4.0.1 h22b1bf0_11 cloog 0.18.0 10 conda-forge cloudpickle 0.7.0 py_0 conda-forge compiler-rt 4.0.1 h5487866_0 conda-forge conda 4.6.4 py36_0 conda-forge conda-env 2.6.0 1 conda-forge constantly 15.1.0 py_0 conda-forge cryptography 2.5 py36ha12b0ac_0 cryptography-vectors 2.5 py_0 conda-forge curl 7.63.0 ha441bb4_1000 cycler 0.10.0 py_1 conda-forge cymem 2.0.2 pypi_0 pypi cython 0.29.5 py36h0a44026_0 conda-forge cytoolz 0.9.0.1 pypi_0 pypi dataclasses 0.6 pypi_0 pypi dbus 1.13.0 h776b7f1_1000 conda-forge decorator 4.3.2 py_0 conda-forge descartes 1.1.0 py_2 conda-forge dill 0.2.9 py36_0 conda-forge docutils 0.14 py36_1001 conda-forge elex 2.4.4 pypi_0 pypi entrypoints 0.3 py36_1000 conda-forge expat 2.2.5 h0a44026_1002 conda-forge fastai 1.0.32 pypi_0 pypi fastprogress 0.1.16 pypi_0 pypi feather-format 0.4.0 pypi_0 pypi fontconfig 2.13.1 h1e4e890_1000 conda-forge freetype 2.9.1 h597ad8a_1005 conda-forge fribidi 1.0.5 h1de35cc_1000 conda-forge future 0.17.1 pypi_0 pypi gast 0.2.1.post0 py_0 conda-forge gcc 4.8.5 8 conda-forge geos 3.7.1 h0a44026_1000 conda-forge gettext 0.19.8.1 hcca000d_1001 conda-forge gfortran_osx-64 4.8.5 h22b1bf0_8 conda-forge ggplot 0.11.5 pypi_0 pypi glib 2.56.2 h67dad55_1001 conda-forge gmp 5.1.2 6 conda-forge graphite2 1.3.13 h2098e52_1000 conda-forge graphviz 2.38.0 hc6cc99f_1011 conda-forge grpcio 1.16.1 py36h044775b_1 gsl 2.4 h1de35cc_4 h5py 2.9.0 nompi_py36h35dc34b_1102 conda-forge harfbuzz 1.9.0 h9889186_1001 conda-forge hdf4 4.2.13 hf3c6af0_1002 conda-forge hdf5 1.10.4 nompi_h646315f_1105 conda-forge html5lib 1.0.1 py_0 conda-forge hyperlink 17.3.1 py_0 conda-forge icu 58.2 h0a44026_1000 conda-forge idna 2.8 py36_1000 conda-forge imagesize 1.1.0 py_0 conda-forge incremental 17.5.0 py_0 conda-forge intel-openmp 2019.1 144 ipykernel 5.1.0 py36h24bf2e0_1002 conda-forge ipython 7.2.0 py36h24bf2e0_1000 conda-forge ipython_genutils 0.2.0 py_1 conda-forge ipywidgets 7.4.2 py_0 conda-forge isl 0.12.2 1 conda-forge isort 4.3.4 pypi_0 pypi jedi 0.13.2 py36_1000 conda-forge jinja2 2.10 py_1 conda-forge jpeg 9c h1de35cc_1001 conda-forge jsonschema 3.0.0a3 py36_1000 conda-forge jupyter 1.0.0 py_1 conda-forge 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 2.2.2 py36_0 conda-forge keras-applications 1.0.4 py_1 conda-forge keras-base 2.2.2 py36_0 keras-preprocessing 1.0.2 py_1 conda-forge keyring 17.1.1 py36_1000 conda-forge kiwisolver 1.0.1 py36h04f5b5a_1002 conda-forge krb5 1.16.1 hddcf347_7 lazy-object-proxy 1.3.1 pypi_0 pypi ld64 274.2 h7c2db76_0 conda-forge libcurl 7.63.0 h051b688_1000 libcxx 4.0.1 h579ed51_0 libcxxabi 4.0.1 hebd6815_0 conda-forge libedit 3.1.20170329 hcfe32e1_1001 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1 conda-forge pandocfilters 1.4.2 py_1 conda-forge pango 1.42.4 h060686c_0 parso 0.3.3 py_0 conda-forge patsy 0.5.1 py_0 conda-forge pbr 5.1.2 py_0 conda-forge pcre 8.42 h378b8a2_0 pexpect 4.6.0 py36_1000 conda-forge pickleshare 0.7.5 py36_1000 conda-forge pillow 5.3.0 pypi_0 pypi pip 18.1 pypi_0 pypi pixman 0.34.0 h1de35cc_1003 conda-forge plac 0.9.6 pypi_0 pypi plotly 3.6.1 py_0 conda-forge plotnine 0.5.1 py_0 conda-forge preshed 2.0.1 pypi_0 pypi progressbar2 3.38.0 pypi_0 pypi 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 py36h0a44026_1001 conda-forge psutil 5.5.0 py36h1de35cc_0 conda-forge pthread-stubs 0.4 h1de35cc_1001 conda-forge ptyprocess 0.6.0 py36_1000 conda-forge pyarrow 0.12.0 pypi_0 pypi pyasn1 0.4.4 py_1 conda-forge pyasn1-modules 0.2.3 py_0 conda-forge pycodestyle 2.5.0 py_0 conda-forge pycosat 0.6.3 py36h1de35cc_1001 conda-forge pycparser 2.19 py_0 conda-forge pyepsg 0.4.0 py_0 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1.6.7 h1de35cc_1000 conda-forge xorg-libxau 1.0.9 h1de35cc_0 conda-forge xorg-libxdmcp 1.1.2 h1de35cc_1007 conda-forge xorg-libxext 1.3.3 h1de35cc_1004 conda-forge xorg-libxrender 0.9.10 h1de35cc_1002 conda-forge xorg-renderproto 0.11.1 h1de35cc_1002 conda-forge xorg-xextproto 7.3.0 h1de35cc_1002 conda-forge xorg-xproto 7.0.31 h1de35cc_1007 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 zlib 1.2.11 h1de35cc_1004 conda-forge zope 1.0 py36_1 zope.interface 4.6.0 py36h1de35cc_1000 conda-forge zstd 1.3.3 1 conda-forge
ocefpaf commented 5 years ago

I don't have a mac to test but based on the conda list you sent looks like you have a mix of channels that may be the culprit. See https://conda-forge.org/docs/conda-forge_gotchas.html#using-multiple-channels for more information on the problem.

Depending on your conda version and the packages you need the solutions can be:

This works for me on Linux with the second suggestion there:

conda create --name TEST python=3.6 netcdf4
conda activate TEST
python -c 'import netCDF4; print(netCDF4.__version__)'
1.4.2
ocefpaf commented 5 years ago

I believe this one was fixed. Please re-open if you are still experiencing this issue.

djgagne commented 5 years ago

I ran into this same problem today. I had to manually update libssh2 to get from netCDF4 import Dataset to work properly. Updating netcdf4 did not trigger an update of libssh2. Is there a way to fix this dependency issue?

ocefpaf commented 5 years ago

@djgagne please open a new issue with the info equested in the issue template so we can debug this.

djgagne commented 5 years ago

See https://github.com/conda-forge/netcdf4-feedstock/issues/88.