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conda-forge / pillow-feedstock

A conda-smithy repository for pillow.
BSD 3-Clause "New" or "Revised" License
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Incorrectly configured PIL shared object file #120

Closed mhearne-usgs closed 2 years ago

mhearne-usgs commented 2 years ago

Solution to issue cannot be found in the documentation.

Issue

We have an application called ShakeMap (https://github.com/usgs/shakemap) that among many other packages, uses scikit learn for a contouring routine. I apologize up front for not being able to isolate this problem to a less complicated installation of packages - I did try, but could not reproduce the error. The error comes up during our tests, when attempting to import the scikit-image measure module. The output from the errors is below:

ImportError while importing test module '/home/mhearne/src/python/shakemap/tests/shakemap/coremods/kml_test.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
../../../miniconda/envs/shakemap/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/shakemap/coremods/kml_test.py:12: in <module>
    from shakemap.coremods.kml import create_kmz
shakemap/coremods/kml.py:23: in <module>
    from shakelib.plotting.contour import contour
shakelib/plotting/contour.py:8: in <module>
    from skimage import measure
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/skimage/_shared/lazy.py:62: in __getattr__
    return importlib.import_module(f'{package_name}.{name}')
../../../miniconda/envs/shakemap/lib/python3.8/importlib/__init__.py:127: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/skimage/measure/__init__.py:6: in <module>
    from ._polygon import approximate_polygon, subdivide_polygon
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/skimage/measure/_polygon.py:2: in <module>
    from scipy import signal
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/signal/__init__.py:309: in <module>
    from . import _sigtools, windows
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/signal/windows/__init__.py:41: in <module>
    from ._windows import *
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/signal/windows/_windows.py:7: in <module>
    from scipy import linalg, special, fft as sp_fft
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/fft/__init__.py:91: in <module>
    from ._helper import next_fast_len
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/fft/_helper.py:3: in <module>
    from ._pocketfft import helper as _helper
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/fft/_pocketfft/__init__.py:3: in <module>
    from .basic import *
../../../miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/fft/_pocketfft/basic.py:6: in <module>
    from . import pypocketfft as pfft
E   ImportError: /home/mhearne/miniconda/envs/shakemap/lib/python3.8/site-packages/PIL/../../../././libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/mhearne/miniconda/envs/shakemap/lib/python3.8/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-38-x86_64-linux-gnu.so)

Installed packages

# packages in environment at /home/mhearne/miniconda/envs/shakemap:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main
_openmp_mutex             5.1                       1_gnu
_sysroot_linux-64_curr_repodata_hack 3                   haa98f57_10
affine                    2.3.0              pyhd3eb1b0_0
alabaster                 0.7.12             pyhd3eb1b0_0
alsa-lib                  1.2.3.2              h166bdaf_0    conda-forge
attrs                     21.4.0             pyhd3eb1b0_0
babel                     2.9.1              pyhd3eb1b0_0
backcall                  0.2.0              pyhd3eb1b0_0
bcrypt                    3.2.0            py38h7b6447c_0
beautifulsoup4            4.11.1           py38h06a4308_0
binutils                  2.36.1               hdd6e379_2    conda-forge
binutils_impl_linux-64    2.36.1               h193b22a_2    conda-forge
binutils_linux-64         2.36                hf3e587d_10    conda-forge
black                     22.3.0             pyhd8ed1ab_0    conda-forge
blas                      1.0                    openblas
blosc                     1.21.1               hd32f23e_0    conda-forge
boost-cpp                 1.74.0               h312852a_4    conda-forge
bottleneck                1.3.4            py38hce1f21e_0
brotli                    1.0.9                he6710b0_2
brotlipy                  0.7.0           py38h27cfd23_1003
brunsli                   0.1                  h2531618_0
bzip2                     1.0.8                h7b6447c_0
c-ares                    1.18.1               h7f8727e_0
c-blosc2                  2.0.4                h5f21a17_1    conda-forge
c-compiler                1.4.2                h166bdaf_0    conda-forge
ca-certificates           2022.4.26            h06a4308_0
cached-property           1.5.2                      py_0
cairo                     1.16.0               hf32fb01_1
cartopy                   0.20.1           py38h4de569d_2    conda-forge
certifi                   2022.5.18.1      py38h06a4308_0
cffi                      1.15.0           py38hd667e15_1
cfitsio                   4.0.0                h9a35b8e_0    conda-forge
cftime                    1.5.1.1          py38hce1f21e_0
charls                    2.2.0                h2531618_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py38h06a4308_0
click-plugins             1.1.1              pyhd3eb1b0_0
cligj                     0.7.2            py38h06a4308_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorama                  0.4.4              pyhd3eb1b0_0
commonmark                0.9.1              pyhd3eb1b0_0
configobj                 5.0.6            py38h06a4308_1
coverage                  6.3.2            py38h7f8727e_0
cryptography              37.0.1           py38h9ce1e76_0
curl                      7.82.0               h7f8727e_0
cycler                    0.11.0             pyhd3eb1b0_0
cython                    0.29.28          py38h295c915_0
cytoolz                   0.11.0           py38h7b6447c_0
dask-core                 2022.5.0         py38h06a4308_0
dataclasses               0.8                pyh6d0b6a4_7
dbus                      1.13.18              hb2f20db_0
decorator                 5.1.1              pyhd3eb1b0_0
defusedxml                0.7.1              pyhd3eb1b0_0
descartes                 1.1.0                    py38_0
docutils                  0.18.1           py38h06a4308_2
et_xmlfile                1.1.0            py38h06a4308_0
expat                     2.4.4                h295c915_0
fiona                     1.8.20           py38hbb147eb_2    conda-forge
flake8                    4.0.1              pyhd3eb1b0_1
font-ttf-dejavu-sans-mono 2.37                 hd3eb1b0_0
font-ttf-inconsolata      2.001                hcb22688_0
font-ttf-source-code-pro  2.030                hd3eb1b0_0
font-ttf-ubuntu           0.83                 h8b1ccd4_0
fontconfig                2.13.96              ha180cfb_0    conda-forge
fonts-anaconda            1                    h8fa9717_0
fonts-conda-ecosystem     1                    hd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.11.0               h70c0345_0
freexl                    1.0.6                h27cfd23_0
fsspec                    2022.3.0         py38h06a4308_0
future                    0.18.2                   py38_1
gcc                       10.3.0              he2824d0_10    conda-forge
gcc_impl_linux-64         10.3.0              hf2f2afa_16    conda-forge
gcc_linux-64              10.3.0              hc39de41_10    conda-forge
gdal                      3.3.3            py38hcf2042a_2    conda-forge
geos                      3.10.0               h9c3ff4c_0    conda-forge
geotiff                   1.7.0                hcfb7246_3    conda-forge
gettext                   0.21.0               hf68c758_0
giflib                    5.2.1                h7b6447c_0
glib                      2.68.4               h9c3ff4c_0    conda-forge
glib-tools                2.68.4               h9c3ff4c_0    conda-forge
greenlet                  1.1.1            py38h295c915_0
gst-plugins-base          1.18.5               hf529b03_0    conda-forge
gstreamer                 1.18.5               h76c114f_0    conda-forge
h5py                      3.6.0           nompi_py38hfbb2109_100    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2386368_104    conda-forge
icu                       68.2                 h9c3ff4c_0    conda-forge
idna                      3.3                pyhd3eb1b0_0
imagecodecs               2021.11.20       py38h678ac2f_1    conda-forge
imageio                   2.9.0              pyhd3eb1b0_0
imagesize                 1.3.0              pyhd3eb1b0_0
impactutils               0.8.40             pyhd8ed1ab_1    conda-forge
importlib-metadata        4.11.3           py38h06a4308_0
iniconfig                 1.1.1              pyhd3eb1b0_0
ipython                   7.29.0           py38hb070fc8_0
jbig                      2.1                  hdba287a_0
jedi                      0.18.1           py38h06a4308_1
jinja2                    3.0.3              pyhd3eb1b0_0
jpeg                      9e                   h7f8727e_0
json-c                    0.15                 h98cffda_0    conda-forge
jxrlib                    1.1                  h7b6447c_2
kealib                    1.4.14               h87e4c3c_3    conda-forge
kernel-headers_linux-64   3.10.0              h57e8cba_10
kiwisolver                1.4.2            py38h295c915_0
krb5                      1.19.2               hac12032_0
lcms2                     2.12                 h3be6417_0
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h295c915_0
libaec                    1.0.6                h9c3ff4c_0    conda-forge
libblas                   3.9.0           15_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h166bdaf_7    conda-forge
libbrotlidec              1.0.9                h166bdaf_7    conda-forge
libbrotlienc              1.0.9                h166bdaf_7    conda-forge
libcblas                  3.9.0           15_linux64_openblas    conda-forge
libclang                  11.1.0          default_ha53f305_1    conda-forge
libcomcat                 2.0.16             pyhd8ed1ab_2    conda-forge
libcurl                   7.82.0               h0b77cf5_0
libdap4                   3.20.6               hd7c4107_2    conda-forge
libdeflate                1.8                  h7f8727e_5
libedit                   3.1.20210910         h7f8727e_0
libev                     4.33                 h7f8727e_1
libevent                  2.1.10               h9b69904_4    conda-forge
libffi                    3.3                  he6710b0_2
libgcc-devel_linux-64     10.3.0              he6cfe16_16    conda-forge
libgcc-ng                 11.2.0               h1234567_1
libgdal                   3.3.3                h18e3bf0_2    conda-forge
libgfortran-ng            11.2.0               h00389a5_1
libgfortran5              11.2.0               h1234567_1
libglib                   2.68.4               h3e27bee_0    conda-forge
libgomp                   11.2.0               h1234567_1
libiconv                  1.16                 h7f8727e_2
libkml                    1.3.0             h238a007_1014    conda-forge
liblapack                 3.9.0           15_linux64_openblas    conda-forge
libllvm11                 11.1.0               h3826bc1_1
libnetcdf                 4.8.1           nompi_h329d8a1_102    conda-forge
libnghttp2                1.46.0               hce63b2e_0
libnsl                    2.0.0                h7f98852_0    conda-forge
libogg                    1.3.5                h27cfd23_1
libopenblas               0.3.20               h043d6bf_1
libopus                   1.3.1                h7b6447c_0
libpng                    1.6.37               hbc83047_0
libpq                     13.5                 hd57d9b9_1    conda-forge
librttopo                 1.1.0                h0ad649c_7    conda-forge
libsanitizer              10.3.0              h26c7422_16    conda-forge
libsodium                 1.0.18               h7b6447c_0
libspatialite             5.0.1               h1d9e4f1_10    conda-forge
libssh2                   1.10.0               h8f2d780_0
libstdcxx-ng              11.2.0               h1234567_1
libtiff                   4.3.0                h6f004c6_2    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libvorbis                 1.3.7                h7b6447c_0
libwebp                   1.2.2                h55f646e_0
libwebp-base              1.2.2                h7f8727e_0
libxcb                    1.15                 h7f8727e_0
libxkbcommon              1.0.3                he3ba5ed_0    conda-forge
libxml2                   2.9.12               h72842e0_0    conda-forge
libxslt                   1.1.33               h15afd5d_2    conda-forge
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h166bdaf_1014    conda-forge
libzopfli                 1.0.3                he6710b0_0
llvm-openmp               8.0.1                hc9558a2_0    conda-forge
locket                    1.0.0            py38h06a4308_0
lockfile                  0.12.2           py38h06a4308_0
lxml                      4.5.1            py38hefd8a0e_0
lz4-c                     1.9.3                h295c915_1
mapio                     0.7.31             pyhd8ed1ab_2    conda-forge
markupsafe                2.1.1            py38h7f8727e_0
matplotlib                3.5.1            py38h06a4308_1
matplotlib-base           3.5.1            py38ha18d171_1
matplotlib-inline         0.1.2              pyhd3eb1b0_2
mccabe                    0.7.0              pyhd3eb1b0_0
more-itertools            8.12.0             pyhd3eb1b0_0
multidict                 5.2.0            py38h7f8727e_2
munch                     2.5.0              pyhd3eb1b0_0
munkres                   1.1.4                      py_0
mypy_extensions           0.4.3            py38h06a4308_1
mysql-common              8.0.27               ha770c72_3    conda-forge
mysql-libs                8.0.27               hfa10184_3    conda-forge
ncurses                   6.3                  h7f8727e_2
netcdf4                   1.5.7            py38ha0f2276_1
networkx                  2.7.1              pyhd3eb1b0_0
nspr                      4.33                 h295c915_0
nss                       3.74                 h0370c37_0
numexpr                   2.8.1            py38hecfb737_0
numpy                     1.21.0           py38h9894fe3_0    conda-forge
obspy                     1.3.0            py38h3ec907f_0    conda-forge
openjpeg                  2.4.0                h3ad879b_0
openmp                    8.0.1                         0    conda-forge
openpyxl                  3.0.9              pyhd3eb1b0_0
openquake-engine          3.12.1                   pypi_0    pypi
openssl                   1.1.1o               h7f8727e_0
packaging                 21.3               pyhd3eb1b0_0
pandas                    1.4.2            py38h295c915_0
paramiko                  2.8.1              pyhd3eb1b0_0
parso                     0.8.3              pyhd3eb1b0_0
partd                     1.2.0              pyhd3eb1b0_1
pathspec                  0.9.0              pyhd8ed1ab_0    conda-forge
pcre                      8.45                 h295c915_0
pexpect                   4.8.0                    py38_0
pickleshare               0.7.5                 py38_1000
pillow                    9.0.1            py38h22f2fdc_0
pip                       22.1.2                   pypi_0    pypi
pixman                    0.40.0               h7f8727e_1
platformdirs              2.4.0              pyhd3eb1b0_0
pluggy                    0.13.1           py38h06a4308_0
poppler                   21.09.0              ha39eefc_3    conda-forge
poppler-data              0.4.11               h06a4308_0
postgresql                13.5                 h2510834_1    conda-forge
proj                      8.1.1                h277dcde_2    conda-forge
prompt-toolkit            3.0.20             pyhd3eb1b0_0
ps2ff                     1.5.2                      py_1    conda-forge
psutil                    5.8.0            py38h27cfd23_1
ptyprocess                0.7.0              pyhd3eb1b0_2
py                        1.11.0             pyhd3eb1b0_0
pycodestyle               2.8.0              pyhd3eb1b0_0
pycparser                 2.21               pyhd3eb1b0_0
pycrypto                  2.6.1           py38h7b6447c_10
pyflakes                  2.4.0              pyhd3eb1b0_0
pygments                  2.11.2             pyhd3eb1b0_0
pynacl                    1.4.0            py38h7b6447c_1
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.4              pyhd3eb1b0_0
pyproj                    3.2.1            py38h80797bf_2    conda-forge
pyqt                      5.12.3           py38h578d9bd_8    conda-forge
pyqt-impl                 5.12.3           py38h0ffb2e6_8    conda-forge
pyqt5-sip                 4.19.18          py38h709712a_8    conda-forge
pyqtchart                 5.12             py38h7400c14_8    conda-forge
pyqtwebengine             5.12.1           py38h7400c14_8    conda-forge
pyshp                     2.1.3              pyhd3eb1b0_0
pysocks                   1.7.1            py38h06a4308_0
pytest                    6.2.4            py38h06a4308_2
pytest-azurepipelines     0.8.0                      py_0
pytest-cov                2.12.1             pyhd3eb1b0_0
pytest-faulthandler       2.0.1                      py_0    conda-forge
python                    3.8.13               h12debd9_0
python-daemon             2.3.0            py38h06a4308_3
python-dateutil           2.8.2              pyhd3eb1b0_0
python_abi                3.8                      2_cp38    conda-forge
pytz                      2022.1           py38h06a4308_0
pywavelets                1.3.0            py38h7f8727e_0
pyyaml                    6.0              py38h7f8727e_1
pyzmq                     22.3.0           py38h295c915_2
qt                        5.12.9               hda022c4_4    conda-forge
rasterio                  1.2.10           py38hfd64e68_0    conda-forge
readline                  8.1.2                h7f8727e_1
requests                  2.27.1             pyhd3eb1b0_0
rope                      0.22.0             pyhd3eb1b0_0
scikit-image              0.19.2           py38h51133e4_0
scipy                     1.8.1            py38h1ee437e_0    conda-forge
setuptools                61.2.0           py38h06a4308_0
shakemap                  0.0.0                     dev_0    <develop>
shapely                   1.8.0            py38hf7953bd_2    conda-forge
simplekml                 1.3.6              pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyhd3eb1b0_1
snappy                    1.1.9                h295c915_0
snowballstemmer           2.2.0              pyhd3eb1b0_0
snuggs                    1.4.7              pyhd3eb1b0_0
soupsieve                 2.3.1              pyhd3eb1b0_0
sphinx                    5.0.1              pyh6c4a22f_0    conda-forge
sphinx-argparse           0.3.1              pyhd8ed1ab_0    conda-forge
sphinxcontrib-applehelp   1.0.2              pyhd3eb1b0_0
sphinxcontrib-devhelp     1.0.2              pyhd3eb1b0_0
sphinxcontrib-htmlhelp    2.0.0              pyhd3eb1b0_0
sphinxcontrib-jsmath      1.0.1              pyhd3eb1b0_0
sphinxcontrib-qthelp      1.0.3              pyhd3eb1b0_0
sphinxcontrib-serializinghtml 1.1.5              pyhd3eb1b0_0
sqlalchemy                1.4.32           py38h7f8727e_0
sqlite                    3.38.2               hc218d9a_0
strec                     2.1.8              pyhd8ed1ab_1    conda-forge
sysroot_linux-64          2.17                h57e8cba_10
tifffile                  2021.7.2           pyhd3eb1b0_2
tiledb                    2.3.4                he87e0bf_0    conda-forge
tk                        8.6.11               h1ccaba5_0
toml                      0.10.2             pyhd3eb1b0_0
tomli                     1.2.2              pyhd3eb1b0_0
toolz                     0.11.2             pyhd3eb1b0_0
tornado                   6.1              py38h27cfd23_0
traitlets                 5.1.1              pyhd3eb1b0_0
typed-ast                 1.4.3            py38h7f8727e_1
typing_extensions         4.1.1              pyh06a4308_0
tzcode                    2022a                h166bdaf_0    conda-forge
tzdata                    2022a                hda174b7_0
urllib3                   1.26.9           py38h06a4308_0
vcrpy                     4.1.1                    py38_0
versioneer                0.22               pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.5              pyhd3eb1b0_0
wheel                     0.37.1             pyhd3eb1b0_0
wrapt                     1.13.3           py38h7f8727e_2
xerces-c                  3.2.3                h9d8b166_3    conda-forge
xlrd                      2.0.1              pyhd3eb1b0_0
xlsxwriter                3.0.3              pyhd3eb1b0_0
xlwt                      1.3.0                    py38_0
xz                        5.2.5                h7f8727e_1
yaml                      0.2.5                h7b6447c_0
yapf                      0.31.0             pyhd3eb1b0_0
yarl                      1.6.3            py38h27cfd23_0
zeromq                    4.3.4                h2531618_0
zfp                       0.5.5                h295c915_6
zipp                      3.8.0            py38h06a4308_0
zlib                      1.2.11            h166bdaf_1014    conda-forge
zstd                      1.5.0                ha4553b6_1

Environment info

conda info

     active environment : shakemap
    active env location : /home/mhearne/miniconda/envs/shakemap
            shell level : 1
       user config file : /home/mhearne/.condarc
 populated config files : /home/mhearne/.condarc
          conda version : 4.12.0
    conda-build version : not installed
         python version : 3.9.7.final.0
       virtual packages : __linux=5.10.16.3=0
                          __glibc=2.31=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /home/mhearne/miniconda  (writable)
      conda av data dir : /home/mhearne/miniconda/etc/conda
  conda av metadata url : None
           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
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/mhearne/miniconda/pkgs
                          /home/mhearne/.conda/pkgs
       envs directories : /home/mhearne/miniconda/envs
                          /home/mhearne/.conda/envs
               platform : linux-64
             user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.7 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.4 glibc/2.31
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
jakirkham commented 2 years ago

Sorry not following why this is on the scikit-learn issue tracker (doesn't appear to be installed in the environment). Maybe it should be on scikit-image. Though as it is PIL, it is more likely an issue with Pillow. Going to move to that feedstock

h-vetinari commented 2 years ago

A lot of your packages are not from conda-forge, making it much harder to diagnose. Can you try

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

and see if the issue still persists.

hmaarrfk commented 2 years ago

Closed since we need more info from original poster