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conda-forge / fiona-feedstock

A conda-smithy repository for fiona.
BSD 3-Clause "New" or "Revised" License
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libzstd.so.1 not found #147

Closed markmuetz closed 4 years ago

markmuetz commented 4 years ago

Issue:

After performing a conda update, the shared object libzstd.so.1 could not be found.

~/.conda/envs/basmati_env/lib/python3.7/site-packages/fiona/collection.py in <module>
      7
      8 from fiona import compat, vfs
----> 9 from fiona.ogrext import Iterator, ItemsIterator, KeysIterator
     10 from fiona.ogrext import Session, WritingSession
     11 from fiona.ogrext import buffer_to_virtual_file, remove_virtual_file, GEOMETRY_TYPES

ImportError: libzstd.so.1: cannot open shared object file: No such file or directory

ldd shows this is needed by ogrext.cpython-37m-x86_64-linux-gnu.so

$ ldd ogrext.cpython-37m-x86_64-linux-gnu.so |grep libzstd
        libzstd.so.1 => /home/users/mmuetz/.conda/envs/basmati_env/lib/python3.7/site-packages/fiona/./../../.././libzstd.so.1 (0x00007f305a518000)

Fix is easy: go to /lib/ and

ln -s libzstd.so.1.3.7 libzstd.so.1

On OS:

$ cat /etc/redhat-release 
Red Hat Enterprise Linux Server release 6.10 (Santiago)


Environment (conda list):

``` $ conda list # packages in environment at /home/users/mmuetz/.conda/envs/basmati_env: # # Name Version Build Channel _libgcc_mutex 0.1 main affine 2.3.0 py_0 conda-forge antlr-python-runtime 4.7.2 py37_1000 conda-forge asn1crypto 1.2.0 py37_0 conda-forge attrs 19.3.0 py_0 conda-forge backcall 0.1.0 py37_0 basmati 0.1.0 dev_0 blas 1.0 openblas conda-forge bokeh 1.3.4 py37_0 conda-forge boost-cpp 1.67.0 h14c3975_4 bzip2 1.0.8 h7b6447c_0 ca-certificates 2019.10.16 0 cairo 1.16.0 h18b612c_1001 conda-forge cartopy 0.17.0 py37he1be148_1005 conda-forge certifi 2019.9.11 py37_0 cf-units 2.1.3 py37hc1659b7_0 conda-forge cffi 1.13.0 py37h2e261b9_0 cfitsio 3.470 hb60a0a2_2 conda-forge cftime 1.0.3.4 py37hdd07704_1001 chardet 3.0.4 py37_1003 conda-forge click 7.0 py37_0 click-plugins 1.1.1 py_0 conda-forge cligj 0.5.0 py37_0 cloudpickle 1.2.2 py_0 conda-forge configparser 4.0.2 pypi_0 pypi cryptography 2.8 py37h1ba5d50_0 curl 7.65.3 hbc83047_0 cycler 0.10.0 py37_0 cytoolz 0.10.0 py37h7b6447c_0 dask 2.6.0 py_0 conda-forge dask-core 2.6.0 py_0 conda-forge dbus 1.13.6 he372182_0 conda-forge decorator 4.4.0 py37_1 descartes 1.1.0 py_3 conda-forge distributed 2.6.0 py_0 conda-forge expat 2.2.6 he6710b0_0 fiona 1.8.6 py37h5f563d9_4 conda-forge fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.9.1 h8a8886c_1 freexl 1.0.5 h14c3975_0 fsspec 0.5.2 py_0 conda-forge gdal 2.4.2 py37h5f563d9_5 conda-forge geopandas 0.4.1 py_0 geos 3.7.2 he1b5a44_1 conda-forge geotiff 1.5.1 h560c3f3_2 conda-forge gettext 0.19.8.1 hd7bead4_3 giflib 5.1.7 h516909a_1 conda-forge glib 2.58.3 h6f030ca_1002 conda-forge gst-plugins-base 1.14.5 h0935bb2_0 conda-forge gstreamer 1.14.5 h36ae1b5_0 conda-forge hdf4 4.2.13 h3ca952b_2 hdf5 1.10.5 nompi_h3c11f04_1103 conda-forge heapdict 1.0.1 py_0 conda-forge icu 58.2 h9c2bf20_1 idna 2.8 py37_0 ipdb 0.12.2 py_0 conda-forge ipython 7.8.0 py37h39e3cac_0 ipython_genutils 0.2.0 py37_0 iris 2.2.1 py37_0 conda-forge jedi 0.15.1 py37_0 conda-forge jinja2 2.10.3 py_0 conda-forge jpeg 9c h14c3975_1001 conda-forge json-c 0.13.1 h1bed415_0 kealib 1.4.10 h58c409b_1005 conda-forge kiwisolver 1.1.0 py37he6710b0_0 krb5 1.16.3 h05b26f9_1001 conda-forge libblas 3.8.0 12_openblas conda-forge libboost 1.67.0 h46d08c1_4 libcblas 3.8.0 12_openblas conda-forge libcurl 7.65.3 h20c2e04_0 libdap4 3.20.2 hd48c02d_1000 conda-forge libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libgdal 2.4.2 h524de44_5 conda-forge libgfortran-ng 7.3.0 hdf63c60_0 libiconv 1.15 h63c8f33_5 libkml 1.3.0 h590aaf7_4 liblapack 3.8.0 12_openblas conda-forge libnetcdf 4.6.2 h303dfb8_1003 conda-forge libopenblas 0.3.7 h6e990d7_1 conda-forge libpng 1.6.37 hbc83047_0 libpq 11.5 hd9ab2ff_1 conda-forge libspatialindex 1.8.5 h20b78c2_2 libspatialite 4.3.0a he1bb1e1_1029 conda-forge libssh2 1.8.2 h1ba5d50_0 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.0.10 h2733197_2 libuuid 2.32.1 h14c3975_1000 conda-forge libxcb 1.13 h1bed415_1 libxml2 2.9.9 hea5a465_1 libxslt 1.1.33 h7d1a2b0_0 locket 0.2.0 py37_1 lxml 4.4.1 py37hefd8a0e_0 lz4-c 1.8.1.2 h14c3975_0 mapclassify 2.0.1 py_0 conda-forge markupsafe 1.1.1 py37h7b6447c_0 matplotlib 2.2.3 py37hb69df0a_0 mock 3.0.5 py37_0 conda-forge msgpack-python 0.6.1 py37hfd86e86_1 munch 2.3.2 py37_0 ncurses 6.1 he6710b0_1 netcdf4 1.5.1.2 py37h73a1b54_1 conda-forge nose 1.3.7 py37_2 conda-forge numpy 1.17.2 py37hf9bf1b6_0 numpy-base 1.17.2 py37h2f8d375_0 olefile 0.46 py37_0 openblas 0.3.7 h6e990d7_1 conda-forge openjpeg 2.3.1 h21c5421_1 conda-forge openssl 1.1.1d h7b6447c_3 owslib 0.18.0 py_0 conda-forge packaging 19.2 py_0 conda-forge pandas 0.25.2 py37he6710b0_0 parso 0.5.1 py_0 conda-forge partd 1.0.0 py_0 conda-forge pcre 8.43 he6710b0_0 pexpect 4.7.0 py37_0 conda-forge pickleshare 0.7.5 py37_0 pillow 6.2.0 py37h34e0f95_0 pip 19.3.1 py37_0 conda-forge pixman 0.38.0 h7b6447c_0 poppler 0.67.0 ha967d66_7 conda-forge poppler-data 0.4.9 0 conda-forge postgresql 11.5 hc63931a_1 conda-forge proj4 6.1.0 he751ad9_2 conda-forge prompt_toolkit 2.0.10 py_0 conda-forge psutil 5.6.3 py37h7b6447c_0 psycopg2 2.8.3 py37h1ba5d50_0 pthread-stubs 0.3 h0ce48e5_1 ptyprocess 0.6.0 py37_0 conda-forge pycparser 2.19 py37_0 pyepsg 0.4.0 py37_0 pygments 2.4.2 py_0 conda-forge pykdtree 1.3.1 py37hdd07704_2 pyke 1.1.1 py37_1000 conda-forge pyopenssl 19.0.0 py37_0 conda-forge pyparsing 2.4.2 py_0 conda-forge pyproj 2.2.1 py37hc44880f_0 conda-forge pyqt 5.9.2 py37h05f1152_2 pyshp 2.1.0 py_0 conda-forge pysocks 1.7.1 py37_0 conda-forge python 3.7.3 h33d41f4_1 conda-forge python-dateutil 2.8.0 py37_0 pytz 2019.3 py_0 conda-forge pyyaml 5.1.2 py37h7b6447c_0 qt 5.9.7 h52cfd70_2 conda-forge rasterio 1.0.28 py37hdff7cfa_0 conda-forge readline 8.0 hf8c457e_0 conda-forge requests 2.22.0 py37_0 conda-forge rtree 0.8.3 py37_0 scipy 1.3.1 py37he2b7bc3_0 setuptools 41.4.0 py37_0 conda-forge shapely 1.6.4 py37hec07ddf_1006 conda-forge sip 4.19.8 py37hf484d3e_0 six 1.12.0 py37_0 snuggs 1.4.7 py_0 conda-forge sortedcontainers 2.1.0 py37_0 sqlalchemy 1.3.10 py37h7b6447c_0 sqlite 3.30.1 h7b6447c_0 tblib 1.4.0 py_0 conda-forge tk 8.6.9 hed695b0_1002 conda-forge toolz 0.10.0 py_0 conda-forge tornado 6.0.3 py37h7b6447c_0 traitlets 4.3.3 py37_0 conda-forge tzcode 2019a h516909a_1002 conda-forge udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge urllib3 1.24.2 py37_0 conda-forge wcwidth 0.1.7 py37_0 wheel 0.33.6 py37_0 conda-forge xerces-c 3.2.2 h780794e_0 xorg-kbproto 1.0.7 h14c3975_1002 conda-forge xorg-libice 1.0.10 h516909a_0 conda-forge xorg-libsm 1.2.3 h84519dc_1000 conda-forge xorg-libx11 1.6.8 h516909a_0 conda-forge xorg-libxau 1.0.9 h14c3975_0 conda-forge xorg-libxdmcp 1.1.3 h516909a_0 conda-forge xorg-libxext 1.3.4 h516909a_0 conda-forge xorg-libxrender 0.9.10 h516909a_1002 conda-forge xorg-renderproto 0.11.1 h14c3975_1002 conda-forge xorg-xextproto 7.3.0 h14c3975_1002 conda-forge xorg-xproto 7.0.31 h14c3975_1007 conda-forge xz 5.2.4 h14c3975_4 yaml 0.1.7 had09818_2 zict 1.0.0 py_0 conda-forge zlib 1.2.11 h7b6447c_3 zstd 1.3.7 h0b5b093_0 ```


Details about conda and system ( conda info ):

``` $ conda info active environment : basmati_env active env location : /home/users/mmuetz/.conda/envs/basmati_env shell level : 3 user config file : /home/users/mmuetz/.condarc populated config files : conda version : 4.6.14 conda-build version : not installed python version : 3.7.3.final.0 base environment : /apps/contrib/jaspy/miniconda_envs/jaspy3.7/m3-4.6.14 (read only) channel URLs : https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch package cache : /apps/contrib/jaspy/miniconda_envs/jaspy3.7/m3-4.6.14/pkgs /home/users/mmuetz/.conda/pkgs envs directories : /home/users/mmuetz/.conda/envs /apps/contrib/jaspy/miniconda_envs/jaspy3.7/m3-4.6.14/envs platform : linux-64 user-agent : conda/4.6.14 requests/2.21.0 CPython/3.7.3 Linux/2.6.32-754.23.1.el6.x86_64 rhel/6.10 glibc/2.12 UID:GID : 7052310:26030 netrc file : None offline mode : False ```
ocefpaf commented 4 years ago

You have a channel mixture. Please see https://conda-forge.org/docs/user/introduction.html#how-can-i-install-packages-from-conda-forge and https://conda-forge.org/docs/user/tipsandtricks.html#how-to-fix-it

markmuetz commented 4 years ago

Thank you. I did not know that such a thing existed.