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conda-forge / geopandas-feedstock

A conda-smithy repository for geopandas.
BSD 3-Clause "New" or "Revised" License
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Geopandas produce "segment fault" #97

Closed crystalandwan closed 1 year ago

crystalandwan commented 2 years ago

Solution to issue cannot be found in the documentation.

Issue

I created a new environment using miniconda, and then installed "geopandas" package. conda create -n ABM2 conda activate ABM2 conda config --env --add channels conda-forge conda config --env --set channel_priority strict conda install python=3 geopandas

The geopandas was successfully installed, and I can import it in Python. But when reading shapefile using geopandas.read_file() function, it produced "segmentation fault".

What I've done:

import geopandas as gpd import os os.chdir("...") os.listdir() ['baltimore_blck2.dbf', ..., 'baltimore_blck.shx'] test = gpd.read_file("baltimore_blck2.shp") Segmentation fault

Installed packages

## Package Plan ##

  environment location: /people/wanh535/.conda/envs/ABM2

  added / updated specs:
    - geopandas
    - python=3

# packages in environment at /people/wanh535/.conda/envs/ABM3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       1_gnu    conda-forge
attrs                     21.4.0             pyhd8ed1ab_0    conda-forge
blosc                     1.21.0               h9c3ff4c_0    conda-forge
boost-cpp                 1.74.0               h6cacc03_7    conda-forge
branca                    0.4.2              pyhd8ed1ab_0    conda-forge
brotli                    1.0.9                h7f98852_6    conda-forge
brotli-bin                1.0.9                h7f98852_6    conda-forge
brotlipy                  0.7.0                    pypi_0    pypi
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.18.1               h7f98852_0    conda-forge
ca-certificates           2021.10.8            ha878542_0    conda-forge
cairo                     1.16.0            ha12eb4b_1010    conda-forge
certifi                   2021.10.8                pypi_0    pypi
cffi                      1.15.0                   pypi_0    pypi
cfitsio                   4.0.0                h9a35b8e_0    conda-forge
charset-normalizer        2.0.12             pyhd8ed1ab_0    conda-forge
click                     8.0.4                    pypi_0    pypi
click-plugins             1.1.1                      py_0    conda-forge
cligj                     0.7.2              pyhd8ed1ab_1    conda-forge
cryptography              36.0.1                   pypi_0    pypi
curl                      7.82.0               h7bff187_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
expat                     2.4.7                h27087fc_0    conda-forge
fiona                     1.8.21                   pypi_0    pypi
folium                    0.12.1.post1       pyhd8ed1ab_1    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 hab24e00_0    conda-forge
fontconfig                2.13.96              h8e229c2_2    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.30.0                   pypi_0    pypi
freetype                  2.10.4               h0708190_1    conda-forge
freexl                    1.0.6                h7f98852_0    conda-forge
gdal                      3.4.1                    pypi_0    pypi
geopandas                 0.10.2             pyhd8ed1ab_1    conda-forge
geopandas-base            0.10.2             pyha770c72_1    conda-forge
geos                      3.10.2               h9c3ff4c_0    conda-forge
geotiff                   1.7.0                h6593c0a_6    conda-forge
gettext                   0.19.8.1          h73d1719_1008    conda-forge
giflib                    5.2.1                h36c2ea0_2    conda-forge
hdf4                      4.2.15               h10796ff_3    conda-forge
hdf5                      1.12.1          nompi_h2386368_104    conda-forge
icu                       69.1                 h9c3ff4c_0    conda-forge
idna                      3.3                pyhd8ed1ab_0    conda-forge
jbig                      2.1               h7f98852_2003    conda-forge
jinja2                    3.0.3              pyhd8ed1ab_0    conda-forge
joblib                    1.1.0              pyhd8ed1ab_0    conda-forge
jpeg                      9e                   h7f98852_0    conda-forge
json-c                    0.15                 h98cffda_0    conda-forge
kealib                    1.4.14               h87e4c3c_3    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.0                    pypi_0    pypi
krb5                      1.19.3               h3790be6_0    conda-forge
lcms2                     2.12                 hddcbb42_0    conda-forge
ld_impl_linux-64          2.36.1               hea4e1c9_2    conda-forge
lerc                      3.0                  h9c3ff4c_0    conda-forge
libblas                   3.9.0           13_linux64_openblas    conda-forge
libbrotlicommon           1.0.9                h7f98852_6    conda-forge
libbrotlidec              1.0.9                h7f98852_6    conda-forge
libbrotlienc              1.0.9                h7f98852_6    conda-forge
libcblas                  3.9.0           13_linux64_openblas    conda-forge
libcurl                   7.82.0               h7bff187_0    conda-forge
libdap4                   3.20.6               hd7c4107_2    conda-forge
libdeflate                1.10                 h7f98852_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 11.2.0              h1d223b6_14    conda-forge
libgdal                   3.4.1                h7b6f8d3_2    conda-forge
libgfortran-ng            11.2.0              h69a702a_14    conda-forge
libgfortran5              11.2.0              h5c6108e_14    conda-forge
libglib                   2.70.2               h174f98d_4    conda-forge
libgomp                   11.2.0              h1d223b6_14    conda-forge
libiconv                  1.16                 h516909a_0    conda-forge
libkml                    1.3.0             h238a007_1014    conda-forge
liblapack                 3.9.0           13_linux64_openblas    conda-forge
libnetcdf                 4.8.1           nompi_hb3fd0d9_101    conda-forge
libnghttp2                1.47.0               h727a467_0    conda-forge
libnsl                    2.0.0                h7f98852_0    conda-forge
libopenblas               0.3.18          pthreads_h8fe5266_0    conda-forge
libpng                    1.6.37               h21135ba_2    conda-forge
libpq                     14.2                 hd57d9b9_0    conda-forge
librttopo                 1.1.0                hf69c175_9    conda-forge
libspatialindex           1.9.3                h9c3ff4c_4    conda-forge
libspatialite             5.0.1               h0e567f8_14    conda-forge
libssh2                   1.10.0               ha56f1ee_2    conda-forge
libstdcxx-ng              11.2.0              he4da1e4_14    conda-forge
libtiff                   4.3.0                h542a066_3    conda-forge
libuuid                   2.32.1            h7f98852_1000    conda-forge
libwebp                   1.2.2                h3452ae3_0    conda-forge
libwebp-base              1.2.2                h7f98852_1    conda-forge
libxcb                    1.13              h7f98852_1004    conda-forge
libxml2                   2.9.12               h885dcf4_1    conda-forge
libzip                    1.8.0                h4de3113_1    conda-forge
libzlib                   1.2.11            h36c2ea0_1013    conda-forge
lz4-c                     1.9.3                h9c3ff4c_1    conda-forge
mapclassify               2.4.3              pyhd8ed1ab_0    conda-forge
markupsafe                2.1.1                    pypi_0    pypi
matplotlib                3.5.1                    pypi_0    pypi
matplotlib-base           3.5.1           py310h23f4a51_0    conda-forge
munch                     2.5.0                      py_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h9c3ff4c_0    conda-forge
networkx                  2.7.1              pyhd8ed1ab_0    conda-forge
nspr                      4.32                 h9c3ff4c_1    conda-forge
nss                       3.74                 hb5efdd6_0    conda-forge
numpy                     1.22.3                   pypi_0    pypi
openjpeg                  2.4.0                hb52868f_1    conda-forge
openssl                   1.1.1l               h7f98852_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.4.1                    pypi_0    pypi
pcre                      8.45                 h9c3ff4c_0    conda-forge
pillow                    9.0.1                    pypi_0    pypi
pip                       22.0.4             pyhd8ed1ab_0    conda-forge
pixman                    0.40.0               h36c2ea0_0    conda-forge
poppler                   21.11.0              ha39eefc_0    conda-forge
poppler-data              0.4.11               hd8ed1ab_0    conda-forge
postgresql                14.2                 h2510834_0    conda-forge
proj                      8.2.1                h277dcde_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 22.0.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.7              pyhd8ed1ab_0    conda-forge
pyproj                    3.3.0                    pypi_0    pypi
pysocks                   1.7.1                    pypi_0    pypi
python                    3.10.2          h85951f9_4_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.10                    2_cp310    conda-forge
pytz                      2021.3             pyhd8ed1ab_0    conda-forge
readline                  8.1                  h46c0cb4_0    conda-forge
requests                  2.27.1             pyhd8ed1ab_0    conda-forge
rtree                     0.9.7                    pypi_0    pypi
scikit-learn              1.0.2                    pypi_0    pypi
scipy                     1.8.0                    pypi_0    pypi
setuptools                60.9.3                   pypi_0    pypi
shapely                   1.8.0                    pypi_0    pypi
six                       1.16.0             pyh6c4a22f_0    conda-forge
sqlite                    3.37.1               h4ff8645_0    conda-forge
threadpoolctl             3.1.0              pyh8a188c0_0    conda-forge
tiledb                    2.6.4                h1e4a385_0    conda-forge
tk                        8.6.12               h27826a3_0    conda-forge
tzcode                    2021e                h7f98852_0    conda-forge
tzdata                    2022a                h191b570_0    conda-forge
unicodedata2              14.0.0                   pypi_0    pypi
urllib3                   1.26.8             pyhd8ed1ab_1    conda-forge
wheel                     0.37.1             pyhd8ed1ab_0    conda-forge
xerces-c                  3.2.3                h8ce2273_4    conda-forge
xorg-kbproto              1.0.7             h7f98852_1002    conda-forge
xorg-libice               1.0.10               h7f98852_0    conda-forge
xorg-libsm                1.2.3             hd9c2040_1000    conda-forge
xorg-libx11               1.7.2                h7f98852_0    conda-forge
xorg-libxau               1.0.9                h7f98852_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xorg-libxext              1.3.4                h7f98852_1    conda-forge
xorg-libxrender           0.9.10            h7f98852_1003    conda-forge
xorg-renderproto          0.11.1            h7f98852_1002    conda-forge
xorg-xextproto            7.3.0             h7f98852_1002    conda-forge
xorg-xproto               7.0.31            h7f98852_1007    conda-forge
xyzservices               2022.3.0           pyhd8ed1ab_0    conda-forge
xz                        5.2.5                h516909a_1    conda-forge
zlib                      1.2.11            h36c2ea0_1013    conda-forge
zstd                      1.5.2                ha95c52a_0    conda-forge

Environment info

active environment : ABM2
    active env location : /.../.../.conda/envs/ABM2
            shell level : 1
       user config file : /.../.../.condarc
 populated config files : /.../.../.conda/envs/ABM2/.condarc
          conda version : 4.10.1
    conda-build version : not installed
         python version : 3.9.1.final.0
       virtual packages : __linux=2.6.32=0
                          __glibc=2.12=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /share/apps/python/miniconda3.9  (read only)
      conda av data dir : /share/apps/python/miniconda3.9/etc/conda
  conda av metadata url : https://repo.anaconda.com/pkgs/main
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          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 : /share/apps/python/miniconda3.9/pkgs
                          /.../.../.conda/pkgs
       envs directories : /.../.../.conda/envs
                          /share/apps/python/miniconda3.9/envs
               platform : linux-64
             user-agent : conda/4.10.1 requests/2.25.1 CPython/3.9.1 Linux/2.6.32-642.6.2.el6.x86_64 rhel/6.6 glibc/2.12
                UID:GID : 277718:100
             netrc file : None
           offline mode : False
mfansler commented 1 year ago

There are PyPI packages leaking into the environment. This is not something that a Conda package can control for. Try cleaning up the system to not have user site-packages. See https://stackoverflow.com/a/70961159/570918. Otherwise, this is in the undefined behavior category - not a bug.

martinfleis commented 1 year ago

Also, GeoPandas is a pure Python package, it cannot produce a segfault. In this case, the culprit is GDAL or one of its dependencies, which is clearly installed fro PyPI, not conda-forge.