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conda-forge / rasterio-feedstock

A conda-smithy repository for rasterio.
BSD 3-Clause "New" or "Revised" License
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ImportError: dlopen(....../python3.6/site-packages/rasterio/_base.cpython-36m-darwin.so, 2): Symbol not found: _crc32 #161

Closed lwasser closed 4 years ago

lwasser commented 4 years ago

Issue:

šŸ‘‹ hi there @ocefpaf !! me, yet again. i'm running into some issues with rasterio (i think) on MAC. Essentially it's throwing errors for our earthpy build: example

https://travis-ci.org/github/earthlab/earthpy/jobs/680217713#L1887

At first it was working just fine for me locally on my mac. But then i rebuilt the environment and got the following failure when running pytest.

Here is what i've tried so far (each time rebuilding the environment completely):

  1. i've added all packages installed via pip install -r dev-requirements.txt to my conda envt just in case it was a pip / conda forge issue - so i just installed stuff using the envt and conda forge - no pip.
  2. i've updated to python version 3.7 and reinstalled the envt

I'm really open to trying something different. this is oddly mac specific so i'm not sure what else to try but i can test it locally. the travis build instructions are here.

https://github.com/earthlab/earthpy/blob/master/.travis/install.sh

(earthpy-dev) CIRES-EL-LM-020:earthpy leahwasser$ pytest
========================================================== test session starts ==========================================================
platform darwin -- Python 3.7.6, pytest-5.4.1, py-1.8.1, pluggy-0.13.0
rootdir: /Users/leahwasser/Documents/github/0-python/earthpy, inifile: setup.cfg, testpaths: earthpy/tests
plugins: cov-2.8.1
INTERNALERROR> Traceback (most recent call last):
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/main.py", line 191, in wrap_session
INTERNALERROR>     session.exitstatus = doit(config, session) or 0
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/main.py", line 246, in _main
INTERNALERROR>     config.hook.pytest_collection(session=session)
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
INTERNALERROR>     return self._hookexec(self, self.get_hookimpls(), kwargs)
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/manager.py", line 92, in _hookexec
INTERNALERROR>     return self._inner_hookexec(hook, methods, kwargs)
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/manager.py", line 86, in <lambda>
INTERNALERROR>     firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall
INTERNALERROR>     return outcome.get_result()
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
INTERNALERROR>     raise ex[1].with_traceback(ex[2])
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 182, in _multicall
INTERNALERROR>     next(gen)  # first yield
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/warnings.py", line 125, in pytest_collection
INTERNALERROR>     config=config, ihook=config.hook, when="collect", item=None
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/contextlib.py", line 112, in __enter__
INTERNALERROR>     return next(self.gen)
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/warnings.py", line 82, in catch_warnings_for_item
INTERNALERROR>     _setoption(warnings, arg)
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/warnings.py", line 21, in _setoption
INTERNALERROR>     category = wmod._getcategory(category)
INTERNALERROR>   File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/warnings.py", line 266, in _getcategory
INTERNALERROR>     raise _OptionError("invalid module name: %r" % (module,)) from None
INTERNALERROR> warnings._OptionError: invalid module name: 'rasterio.errors'
Traceback (most recent call last):
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/bin/pytest", line 11, in <module>
    sys.exit(main())
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/config/__init__.py", line 125, in main
    config=config
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/manager.py", line 92, in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/manager.py", line 86, in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 208, in _multicall
    return outcome.get_result()
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 187, in _multicall
    res = hook_impl.function(*args)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/main.py", line 240, in pytest_cmdline_main
    return wrap_session(config, _main)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/main.py", line 229, in wrap_session
    session=session, exitstatus=session.exitstatus
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/hooks.py", line 286, in __call__
    return self._hookexec(self, self.get_hookimpls(), kwargs)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/manager.py", line 92, in _hookexec
    return self._inner_hookexec(hook, methods, kwargs)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/manager.py", line 86, in <lambda>
    firstresult=hook.spec.opts.get("firstresult") if hook.spec else False,
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 203, in _multicall
    gen.send(outcome)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/terminal.py", line 716, in pytest_sessionfinish
    outcome.get_result()
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 80, in get_result
    raise ex[1].with_traceback(ex[2])
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/pluggy/callers.py", line 182, in _multicall
    next(gen)  # first yield
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/warnings.py", line 143, in pytest_sessionfinish
    config=config, ihook=config.hook, when="config", item=None
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/contextlib.py", line 112, in __enter__
    return next(self.gen)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/warnings.py", line 82, in catch_warnings_for_item
    _setoption(warnings, arg)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/site-packages/_pytest/warnings.py", line 21, in _setoption
    category = wmod._getcategory(category)
  File "/Users/leahwasser/miniconda3/envs/earthpy-dev/lib/python3.7/warnings.py", line 266, in _getcategory
    raise _OptionError("invalid module name: %r" % (module,)) from None
warnings._OptionError: invalid module name: 'rasterio.errors'

To recreate, following this:

https://github.com/earthlab/earthpy/blob/master/CONTRIBUTING.rst

But note that this failure is occuring on multiple builds right now with spatial dependencies.

A WORKING BUILD:

JUST FOR GIGGLES - here is my local environment BEFORE updating when all was running nicely. i took a "snapshot" of the envt specs just in case it would help.

CURRENT INSTALL:

(earthpy-dev) CIRES-EL-LM-020:earthpy leahwasser$ conda list
# packages in environment at /Users/leahwasser/miniconda3/envs/earthpy-dev:
#
# Name                    Version                   Build  Channel
affine                    2.3.0                      py_0    conda-forge
alabaster                 0.7.12                   pypi_0    pypi
argh                      0.26.2                   pypi_0    pypi
aspy-yaml                 1.3.0                    pypi_0    pypi
atomicwrites              1.3.0                    pypi_0    pypi
attrs                     19.3.0                     py_0    conda-forge
babel                     2.7.0                    pypi_0    pypi
boost-cpp                 1.70.0               h75728bb_2    conda-forge
bumpversion               0.5.3                    pypi_0    pypi
bzip2                     1.0.8                h0b31af3_2    conda-forge
ca-certificates           2020.4.5.1           hecc5488_0    conda-forge
cairo                     1.16.0            he1c11cd_1002    conda-forge
certifi                   2020.4.5.1       py36h9f0ad1d_0    conda-forge
cfgv                      2.0.1                    pypi_0    pypi
cfitsio                   3.470                h84d2f63_2    conda-forge
chardet                   3.0.4                    pypi_0    pypi
click                     7.0                        py_0    conda-forge
click-plugins             1.1.1                      py_0    conda-forge
cligj                     0.5.0                      py_0    conda-forge
cloudpickle               1.2.2                      py_1    conda-forge
codecov                   2.0.22                   pypi_0    pypi
coverage                  4.5.4                    pypi_0    pypi
curl                      7.65.3               h22ea746_0    conda-forge
cycler                    0.10.0                     py_2    conda-forge
cytoolz                   0.10.1           py36h0b31af3_0    conda-forge
dask-core                 2.9.1                      py_0    conda-forge
decorator                 4.4.1                      py_0    conda-forge
docutils                  0.15.2                   pypi_0    pypi
earthpy                   0.8.0                     dev_0    <develop>
entrypoints               0.3             py36h9f0ad1d_1001    conda-forge
expat                     2.2.9                h4a8c4bd_2    conda-forge
filelock                  3.0.12                   pypi_0    pypi
fiona                     1.8.13           py36he71f6a4_0    conda-forge
flake8                    3.7.9            py36h9f0ad1d_1    conda-forge
fontconfig                2.13.1            h6b1039f_1001    conda-forge
freetype                  2.10.0               h24853df_1    conda-forge
freexl                    1.0.5             h1de35cc_1002    conda-forge
gdal                      3.0.3            py36h97c3584_0    conda-forge
geopandas                 0.7.0                      py_1    conda-forge
geos                      3.8.0                h4a8c4bd_0    conda-forge
geotiff                   1.5.1                hc9fff18_8    conda-forge
gettext                   0.19.8.1          h46ab8bc_1002    conda-forge
giflib                    5.2.1                h0b31af3_1    conda-forge
glib                      2.58.3          py36h577aef8_1002    conda-forge
hdf4                      4.2.13            h84186c3_1003    conda-forge
hdf5                      1.10.5          nompi_h3e39495_1104    conda-forge
icu                       64.2                 h6de7cb9_1    conda-forge
identify                  1.4.7                    pypi_0    pypi
idna                      2.8                      pypi_0    pypi
imageio                   2.6.1                    py36_0    conda-forge
imagesize                 1.1.0                    pypi_0    pypi
importlib-metadata        1.5.2                    pypi_0    pypi
importlib-resources       1.0.2                    pypi_0    pypi
jinja2                    2.10.3                   pypi_0    pypi
jpeg                      9c                h1de35cc_1001    conda-forge
json-c                    0.13.1            h1de35cc_1001    conda-forge
kealib                    1.4.10            h6659575_1005    conda-forge
kiwisolver                1.1.0            py36ha1b3eb9_0    conda-forge
krb5                      1.16.4               h1752a42_0    conda-forge
libblas                   3.8.0               14_openblas    conda-forge
libcblas                  3.8.0               14_openblas    conda-forge
libcurl                   7.65.3               h16faf7d_0    conda-forge
libcxx                    9.0.1                         1    conda-forge
libdap4                   3.20.4               habf5908_0    conda-forge
libedit                   3.1.20170329      hcfe32e1_1001    conda-forge
libffi                    3.2.1             h6de7cb9_1006    conda-forge
libgdal                   3.0.3                hf96e369_0    conda-forge
libgfortran               4.0.0                         2    conda-forge
libiconv                  1.15              h01d97ff_1005    conda-forge
libkml                    1.3.0             hed7d534_1010    conda-forge
liblapack                 3.8.0               14_openblas    conda-forge
libnetcdf                 4.7.3           nompi_hec86efb_100    conda-forge
libopenblas               0.3.7                h3d69b6c_7    conda-forge
libpng                    1.6.37               h2573ce8_0    conda-forge
libpq                     12.1                 h31a01ba_0    conda-forge
libspatialindex           1.9.3                h4a8c4bd_1    conda-forge
libspatialite             4.3.0a            h9c28a66_1034    conda-forge
libssh2                   1.8.2                hcdc9a53_2    conda-forge
libtiff                   4.1.0                ha78913b_3    conda-forge
libwebp                   1.0.2                hd3bf737_5    conda-forge
libxml2                   2.9.10               h53d96d6_0    conda-forge
livereload                2.6.1                    pypi_0    pypi
llvm-openmp               9.0.1                h28b9765_1    conda-forge
lz4-c                     1.8.3             h6de7cb9_1001    conda-forge
m2r                       0.2.1                    pypi_0    pypi
markupsafe                1.1.1                    pypi_0    pypi
matplotlib                3.1.2                    py36_1    conda-forge
matplotlib-base           3.1.2            py36h11da6c2_1    conda-forge
mccabe                    0.6.1                      py_1    conda-forge
mistune                   0.8.4                    pypi_0    pypi
more-itertools            7.2.0                    pypi_0    pypi
multidict                 4.5.2                    pypi_0    pypi
munch                     2.5.0                      py_0    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
networkx                  2.4                        py_0    conda-forge
nodeenv                   1.3.3                    pypi_0    pypi
numpy                     1.17.3           py36hde6bac1_0    conda-forge
olefile                   0.46                       py_0    conda-forge
openjpeg                  2.3.1                hcdae239_3    conda-forge
openssl                   1.1.1g               h0b31af3_0    conda-forge
packaging                 19.2                     pypi_0    pypi
pandas                    0.25.3           py36h4f17bb1_0    conda-forge
pathtools                 0.1.2                    pypi_0    pypi
pcre                      8.43                 h4a8c4bd_0    conda-forge
pillow                    7.0.0            py36h918e99a_0    conda-forge
pip                       19.3.1                   py36_0    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
pluggy                    0.13.0                   pypi_0    pypi
poppler                   0.67.0               h16886b5_8    conda-forge
poppler-data              0.4.9                         1    conda-forge
port-for                  0.3.1                    pypi_0    pypi
postgresql                12.1                 h26bc10f_0    conda-forge
pre-commit                1.21.0                   pypi_0    pypi
proj                      6.3.0                h773a61f_0    conda-forge
py                        1.8.0                    pypi_0    pypi
pycodestyle               2.5.0                      py_0    conda-forge
pyflakes                  2.1.1                      py_0    conda-forge
pygments                  2.4.2                    pypi_0    pypi
pyparsing                 2.4.6                      py_0    conda-forge
pyproj                    2.4.2.post1      py36hf8af742_1    conda-forge
pytest                    5.4.1                    pypi_0    pypi
pytest-cov                2.7.1                    pypi_0    pypi
pytest-vcr                1.0.2                    pypi_0    pypi
python                    3.6.7             h4285619_1006    conda-forge
python-dateutil           2.8.1                      py_0    conda-forge
python_abi                3.6                     1_cp36m    conda-forge
pytz                      2019.3                     py_0    conda-forge
pywavelets                1.1.1            py36h3b54f70_0    conda-forge
pyyaml                    5.1.2                    pypi_0    pypi
rasterio                  1.1.2            py36he71f6a4_0    conda-forge
readline                  8.0                  hcfe32e1_0    conda-forge
requests                  2.22.0                   pypi_0    pypi
rtree                     0.9.3            py36h7b0cdae_0    conda-forge
scikit-image              0.16.2           py36h4f17bb1_0    conda-forge
scipy                     1.4.1            py36h82752d6_0    conda-forge
setuptools                45.0.0                   py36_1    conda-forge
shapely                   1.6.4           py36h999ffa5_1007    conda-forge
six                       1.14.0                   py36_0    conda-forge
snowballstemmer           2.0.0                    pypi_0    pypi
snuggs                    1.4.7                      py_0    conda-forge
sphinx                    2.4.0                    pypi_0    pypi
sphinx-autobuild          0.7.1                    pypi_0    pypi
sphinx-gallery            0.5.0                    pypi_0    pypi
sphinx-rtd-theme          0.4.3                    pypi_0    pypi
sphinxcontrib-applehelp   1.0.1                    pypi_0    pypi
sphinxcontrib-devhelp     1.0.1                    pypi_0    pypi
sphinxcontrib-htmlhelp    1.0.2                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      1.0.2                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.3                    pypi_0    pypi
sqlite                    3.30.1               h93121df_0    conda-forge
tbb                       2018.0.5             h2d50403_0    conda-forge
tiledb                    1.7.0                hd5e958f_2    conda-forge
tk                        8.6.10               hbbe82c9_0    conda-forge
toml                      0.10.0                   pypi_0    pypi
toolz                     0.10.0                     py_0    conda-forge
tornado                   6.0.3            py36h0b31af3_0    conda-forge
tox                       3.14.6                   pypi_0    pypi
tzcode                    2019a             h01d97ff_1002    conda-forge
urllib3                   1.25.6                   pypi_0    pypi
vcrpy                     2.1.0                    pypi_0    pypi
virtualenv                16.7.7                   pypi_0    pypi
watchdog                  0.9.0                    pypi_0    pypi
wcwidth                   0.1.7                    pypi_0    pypi
wheel                     0.33.6                   py36_0    conda-forge
wrapt                     1.11.2                   pypi_0    pypi
xerces-c                  3.2.2             hbda6038_1004    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
yarl                      1.3.0                    pypi_0    pypi
zipp                      0.6.0                    pypi_0    pypi
zlib                      1.2.11            h0b31af3_1006    conda-forge
zstd                      1.4.4                he7fca8b_1    conda-forge


Environment (conda list):

``` $ conda list (earthpy-dev) CIRES-EL-LM-020:earthpy leahwasser$ conda list # packages in environment at /Users/leahwasser/miniconda3/envs/earthpy-dev: # # Name Version Build Channel affine 2.3.0 py_0 conda-forge alabaster 0.7.12 py_0 conda-forge argh 0.26.2 py37_1001 conda-forge attrs 19.3.0 py_0 conda-forge babel 2.8.0 py_0 conda-forge boost-cpp 1.72.0 hdf9ef73_0 conda-forge brotlipy 0.7.0 py37h9bfed18_1000 conda-forge bumpversion 0.5.3 py_1001 conda-forge bzip2 1.0.8 h0b31af3_2 conda-forge ca-certificates 2020.4.5.1 hecc5488_0 conda-forge cairo 1.16.0 hec6a9b0_1003 conda-forge certifi 2020.4.5.1 py37hc8dfbb8_0 conda-forge cffi 1.14.0 py37h356ff06_0 conda-forge cfgv 3.1.0 py_0 conda-forge cfitsio 3.470 h35c4aa5_3 conda-forge chardet 3.0.4 py37hc8dfbb8_1006 conda-forge click 7.1.1 pyh8c360ce_0 conda-forge click-plugins 1.1.1 py_0 conda-forge cligj 0.5.0 py_0 conda-forge cloudpickle 1.3.0 py_0 conda-forge codecov 2.0.20 pyh9f0ad1d_0 conda-forge coverage 5.1 py37h9bfed18_0 conda-forge cryptography 2.9.2 py37he655712_0 conda-forge curl 7.69.1 h2d98d24_0 conda-forge cycler 0.10.0 py_2 conda-forge cytoolz 0.10.1 py37h0b31af3_0 conda-forge dask-core 2.15.0 py_0 conda-forge decorator 4.4.2 py_0 conda-forge docutils 0.16 py37hc8dfbb8_1 conda-forge editdistance 0.5.3 py37h570ac47_0 conda-forge expat 2.2.9 h4a8c4bd_2 conda-forge filelock 3.0.10 py_0 conda-forge fiona 1.8.13 py37he71f6a4_0 conda-forge fontconfig 2.13.1 h6b1039f_1001 conda-forge freetype 2.10.1 h8da9a1a_0 conda-forge freexl 1.0.5 h1de35cc_1002 conda-forge gdal 3.0.4 py37h08e9697_8 conda-forge geopandas 0.7.0 py_1 conda-forge geos 3.8.1 h4a8c4bd_0 conda-forge geotiff 1.5.1 hd8796ba_10 conda-forge gettext 0.19.8.1 h46ab8bc_1002 conda-forge giflib 5.2.1 h0b31af3_2 conda-forge glib 2.64.2 h577aef8_0 conda-forge hdf4 4.2.13 h84186c3_1003 conda-forge hdf5 1.10.6 nompi_h3e39495_100 conda-forge icu 64.2 h6de7cb9_1 conda-forge identify 1.4.14 pyh9f0ad1d_0 conda-forge idna 2.9 py_1 conda-forge imageio 2.8.0 py_0 conda-forge imagesize 1.2.0 py_0 conda-forge importlib-metadata 1.6.0 py37hc8dfbb8_0 conda-forge importlib_metadata 1.6.0 0 conda-forge jinja2 2.11.2 pyh9f0ad1d_0 conda-forge jpeg 9c h1de35cc_1001 conda-forge json-c 0.13.1 h1de35cc_1001 conda-forge kealib 1.4.13 h40102fb_1 conda-forge kiwisolver 1.2.0 py37ha1cc60f_0 conda-forge krb5 1.17.1 h1752a42_0 conda-forge libblas 3.8.0 16_openblas conda-forge libcblas 3.8.0 16_openblas conda-forge libcurl 7.69.1 hc0b9707_0 conda-forge libcxx 10.0.0 h1af66ff_2 conda-forge libdap4 3.20.6 h8c15375_0 conda-forge libedit 3.1.20170329 hcfe32e1_1001 conda-forge libffi 3.2.1 h4a8c4bd_1007 conda-forge libgdal 3.0.4 h1772500_8 conda-forge libgfortran 4.0.0 2 conda-forge libiconv 1.15 h0b31af3_1006 conda-forge libkml 1.3.0 h169b8f9_1011 conda-forge liblapack 3.8.0 16_openblas conda-forge libnetcdf 4.7.4 nompi_ha11d67f_102 conda-forge libopenblas 0.3.9 h3d69b6c_0 conda-forge libpng 1.6.37 hbbe82c9_1 conda-forge libpq 12.2 h489d428_1 conda-forge libspatialindex 1.9.3 h4a8c4bd_3 conda-forge libspatialite 4.3.0a h658e6c1_1038 conda-forge libssh2 1.8.2 hcdc9a53_2 conda-forge libtiff 4.1.0 h2ae36a8_6 conda-forge libwebp-base 1.1.0 h0b31af3_3 conda-forge libxml2 2.9.10 h53d96d6_0 conda-forge livereload 2.6.1 py_0 conda-forge llvm-openmp 10.0.0 h28b9765_0 conda-forge lz4-c 1.9.2 h4a8c4bd_0 conda-forge markupsafe 1.1.1 py37h9bfed18_1 conda-forge matplotlib 3.2.1 0 conda-forge matplotlib-base 3.2.1 py37hddda452_0 conda-forge more-itertools 8.2.0 py_0 conda-forge munch 2.5.0 py_0 conda-forge ncurses 6.1 h0a44026_1002 conda-forge networkx 2.4 py_1 conda-forge nodeenv 1.3.5 py_0 conda-forge numpy 1.18.1 py37h7687784_1 conda-forge olefile 0.46 py_0 conda-forge openjpeg 2.3.1 h254dc36_3 conda-forge openssl 1.1.1g h0b31af3_0 conda-forge packaging 20.1 py_0 conda-forge pandas 1.0.3 py37h94625e5_1 conda-forge pathtools 0.1.2 py_1 conda-forge pcre 8.44 h4a8c4bd_0 conda-forge pillow 7.1.2 py37hfd78ece_0 conda-forge pip 20.0.2 py_2 conda-forge pixman 0.38.0 h01d97ff_1003 conda-forge pluggy 0.13.0 py37_0 conda-forge poppler 0.87.0 h3232a60_1 conda-forge poppler-data 0.4.9 1 conda-forge port-for 0.4 py_1 conda-forge postgresql 12.2 h62ab893_1 conda-forge pre-commit 2.3.0 py37hc8dfbb8_0 conda-forge proj 7.0.0 hbce2d5c_3 conda-forge py 1.8.1 py_0 conda-forge pycparser 2.20 py_0 conda-forge pygments 2.6.1 py_0 conda-forge pyopenssl 19.1.0 py_1 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyproj 2.6.0 py37hbd4ead9_1 conda-forge pysocks 1.7.1 py37hc8dfbb8_1 conda-forge pytest 5.4.1 py37hc8dfbb8_0 conda-forge pytest-cov 2.8.1 py_0 conda-forge python 3.7.6 h90870a6_5_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.7 1_cp37m conda-forge pytz 2019.3 py_0 conda-forge pywavelets 1.1.1 py37h10e2902_1 conda-forge pyyaml 5.3.1 py37h9bfed18_0 conda-forge rasterio 1.1.3 py37he71f6a4_0 conda-forge readline 8.0 hcfe32e1_0 conda-forge requests 2.23.0 pyh8c360ce_2 conda-forge rtree 0.9.4 py37h8526d28_1 conda-forge scikit-image 0.16.2 py37h4f17bb1_0 conda-forge scipy 1.4.1 py37hce1b9e5_3 conda-forge setuptools 46.1.3 py37hc8dfbb8_0 conda-forge shapely 1.7.0 py37hfcf0db4_3 conda-forge six 1.14.0 py_1 conda-forge snowballstemmer 2.0.0 py_0 conda-forge snuggs 1.4.7 py_0 conda-forge sphinx 3.0.3 py_0 conda-forge sphinx-autobuild 0.7.1 py_2 conda-forge sphinx_rtd_theme 0.4.3 py_0 conda-forge sphinxcontrib-applehelp 1.0.2 py_0 conda-forge sphinxcontrib-devhelp 1.0.2 py_0 conda-forge sphinxcontrib-htmlhelp 1.0.3 py_0 conda-forge sphinxcontrib-jsmath 1.0.1 py_0 conda-forge sphinxcontrib-qthelp 1.0.3 py_0 conda-forge sphinxcontrib-serializinghtml 1.1.4 py_0 conda-forge sqlite 3.30.1 h93121df_0 conda-forge tbb 2018.0.5 h2d50403_0 conda-forge tiledb 1.7.7 h84aa2a7_1 conda-forge tk 8.6.10 hbbe82c9_0 conda-forge toml 0.10.0 py_0 conda-forge toolz 0.10.0 py_0 conda-forge tornado 6.0.4 py37h9bfed18_1 conda-forge tox 3.14.6 py37hc8dfbb8_0 conda-forge tzcode 2020a h0b31af3_0 conda-forge urllib3 1.25.9 py_0 conda-forge virtualenv 16.7.5 py_0 conda-forge watchdog 0.10.2 py37h0b31af3_0 conda-forge wcwidth 0.1.9 pyh9f0ad1d_0 conda-forge wheel 0.34.2 py_1 conda-forge xerces-c 3.2.2 h8f8adb3_1004 conda-forge xz 5.2.5 h0b31af3_0 conda-forge yaml 0.2.4 h0b31af3_0 conda-forge zipp 3.1.0 py_0 conda-forge zlib 1.2.11 h0b31af3_1006 conda-forge zstd 1.4.4 h4b3e974_3 conda-forge ```


Details about conda and system ( conda info ):

``` $ conda info active env location : /Users/leahwasser/miniconda3/envs/earthpy-dev shell level : 2 user config file : /Users/leahwasser/.condarc populated config files : /Users/leahwasser/.condarc conda version : 4.8.3 conda-build version : not installed python version : 3.7.6.final.0 virtual packages : __osx=10.14.6 base environment : /Users/leahwasser/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/osx-64 https://conda.anaconda.org/conda-forge/noarch https://repo.anaconda.com/pkgs/main/osx-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/osx-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /Users/leahwasser/miniconda3/pkgs /Users/leahwasser/.conda/pkgs envs directories : /Users/leahwasser/miniconda3/envs /Users/leahwasser/.conda/envs platform : osx-64 user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.6 Darwin/18.7.0 OSX/10.14.6 UID:GID : 502:20 netrc file : None offline mode : False ```

I'm happy to try anything else that might help with troubleshooting. i'm just not sure what else to try! I hope all is well.

djhoese commented 4 years ago

I'm also seeing this on travis:

>   from rasterio._base import gdal_version
E   ImportError: dlopen(/Users/travis/miniconda/envs/test/lib/python3.8/site-packages/rasterio/_base.cpython-38-darwin.so, 2): Symbol not found: _crc32
E     Referenced from: /Users/travis/miniconda/envs/test/lib/libgdal.26.dylib
E     Expected in: /Users/travis/miniconda/envs/test/lib/libcfitsio.8.dylib
E    in /Users/travis/miniconda/envs/test/lib/libgdal.26.dylib

Relevant travis job: https://travis-ci.org/github/pytroll/satpy/jobs/680364670

lwasser commented 4 years ago

Oh interesting. And you are on python 3.8. Ive tested on 3.6 and 3.7 so it is not the python version!

I downgraded several packages too including gdal to see if I could figure out which upgrade broke things but to no avail.

djhoese commented 4 years ago

Looks like cfitsio had a new release a couple days ago: https://github.com/conda-forge/cfitsio-feedstock

@lwasser Could you try forcing the version to something older. I think this should work:

conda install cfitsio=3.470=2
lwasser commented 4 years ago

@djhoese PROGRESS!

i ran this conda install -c conda-forge cfitsio=3.470=h84d2f63_2

and pytest is running perfectly now!

in my broken build i have this: cfitsio 3.470 h35c4aa5_3

It was funny because i thought that package might be the cuprit but i saw the same version numbers missing the fact that the build is different. So is the solution for now (temporarily) to downgrade our builds to that working build. And in the future perhaps this build will resolve properly?

lwasser commented 4 years ago

@djhoese given this is open in the cfitsio repo, should i close here? just wanted to check that there is nothing to do with rasterio before closing. seems to be on the way to being fixed in the other repo.

ocefpaf commented 4 years ago

wave hi there @ocefpaf !! me, yet again. i'm running into some issues with rasterio (i think) on MAC. Essentially it's throwing errors for our earthpy build: example

Sorry, just got back to work today. Looks like people already found a way forward to fix this.

@djhoese given this is open in the cfitsio repo, should i close here? just wanted to check that there is nothing to do with rasterio before closing. seems to be on the way to being fixed in the other repo.

Yes please. Thanks for the but report!

lwasser commented 4 years ago

šŸ‘‹ @ocefpaf no worries!! and thank you!!

yes i think we did some detective work and it's cfitsio. i'll close for now :) but again happy to test when its needed!!