conda install geopandas python=3.8 error libtbb

[mgsnuno]

Issue: import geopandas fails with python 3.8, libtbb not found. has to be explicitly installed.

Environment (conda list):

``` # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge attrs 19.3.0 py_0 conda-forge boost-cpp 1.72.0 h8e57a91_0 conda-forge bzip2 1.0.8 h516909a_2 conda-forge ca-certificates 2020.4.5.1 hecc5488_0 conda-forge cairo 1.16.0 hcf35c78_1003 conda-forge certifi 2020.4.5.1 py38h32f6830_0 conda-forge cfitsio 3.470 h3eac812_5 conda-forge click 7.1.2 pyh9f0ad1d_0 conda-forge click-plugins 1.1.1 py_0 conda-forge cligj 0.5.0 py_0 conda-forge curl 7.69.1 h33f0ec9_0 conda-forge expat 2.2.9 he1b5a44_2 conda-forge fiona 1.8.13 py38h033e0f6_1 conda-forge fontconfig 2.13.1 h86ecdb6_1001 conda-forge freetype 2.10.2 he06d7ca_0 conda-forge freexl 1.0.5 h14c3975_1002 conda-forge gdal 3.0.4 py38h172510d_10 conda-forge geopandas 0.7.0 py_1 conda-forge geos 3.8.1 he1b5a44_0 conda-forge geotiff 1.6.0 h05acad5_0 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge giflib 5.2.1 h516909a_2 conda-forge glib 2.64.3 h6f030ca_0 conda-forge hdf4 4.2.13 hf30be14_1003 conda-forge hdf5 1.10.6 nompi_h3c11f04_100 conda-forge icu 64.2 he1b5a44_1 conda-forge jpeg 9c h14c3975_1001 conda-forge json-c 0.13.1 hbfbb72e_1002 conda-forge kealib 1.4.13 h33137a7_1 conda-forge krb5 1.17.1 h2fd8d38_0 conda-forge ld_impl_linux-64 2.34 h53a641e_3 conda-forge libblas 3.8.0 16_openblas conda-forge libcblas 3.8.0 16_openblas conda-forge libcurl 7.69.1 hf7181ac_0 conda-forge libdap4 3.20.6 h1d1bd15_0 conda-forge libedit 3.1.20170329 hf8c457e_1001 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgdal 3.0.4 he6a97d6_10 conda-forge libgfortran-ng 7.5.0 hdf63c60_6 conda-forge libiconv 1.15 h516909a_1006 conda-forge libkml 1.3.0 hb574062_1011 conda-forge liblapack 3.8.0 16_openblas conda-forge libnetcdf 4.7.4 nompi_h84807e1_104 conda-forge libopenblas 0.3.9 h5ec1e0e_0 conda-forge libpng 1.6.37 hed695b0_1 conda-forge libpq 12.2 h5513abc_1 conda-forge libspatialindex 1.9.3 he1b5a44_3 conda-forge libspatialite 4.3.0a h2482549_1038 conda-forge libssh2 1.9.0 hab1572f_2 conda-forge libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge libtiff 4.1.0 hc7e4089_6 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libwebp-base 1.1.0 h516909a_3 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.10 hee79883_0 conda-forge llvm-openmp 10.0.0 hc9558a2_0 conda-forge lz4-c 1.9.2 he1b5a44_1 conda-forge munch 2.5.0 py_0 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge numpy 1.18.4 py38h8854b6b_0 conda-forge openjpeg 2.3.1 h981e76c_3 conda-forge openssl 1.1.1g h516909a_0 conda-forge pandas 1.0.3 py38hcb8c335_1 conda-forge pcre 8.44 he1b5a44_0 conda-forge pip 20.1.1 pyh9f0ad1d_0 conda-forge pixman 0.38.0 h516909a_1003 conda-forge poppler 0.87.0 h4190859_1 conda-forge poppler-data 0.4.9 1 conda-forge postgresql 12.2 h8573dbc_1 conda-forge proj 7.0.0 h966b41f_4 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge pyproj 2.6.1.post1 py38h7521cb9_0 conda-forge python 3.8.2 he5300dc_7_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python_abi 3.8 1_cp38 conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge readline 8.0 hf8c457e_0 conda-forge rtree 0.9.4 py38h08f867b_1 conda-forge setuptools 46.4.0 py38h32f6830_0 conda-forge shapely 1.7.0 py38hd168ffb_3 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.30.1 hcee41ef_0 conda-forge tiledb 1.7.7 h8efa9f0_2 conda-forge tk 8.6.10 hed695b0_0 conda-forge tzcode 2020a h516909a_0 conda-forge wheel 0.34.2 py_1 conda-forge xerces-c 3.2.2 h8412b87_1004 conda-forge 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 1.6.9 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 5.2.5 h516909a_0 conda-forge zlib 1.2.11 h516909a_1006 conda-forge zstd 1.4.4 h6597ccf_3 conda-forge ```

Details about conda and system ( conda info ):

``` active environment : testgeopandas active env location : /home/nuno/miniconda3/envs/testgeopandas shell level : 3 user config file : /home/nuno/.condarc populated config files : /home/nuno/.condarc conda version : 4.8.3 conda-build version : not installed python version : 3.7.4.final.0 virtual packages : __glibc=2.31 base environment : /home/nuno/miniconda3 (writable) 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 package cache : /home/nuno/miniconda3/pkgs /home/nuno/.conda/pkgs envs directories : /home/nuno/miniconda3/envs /home/nuno/.conda/envs platform : linux-64 user-agent : conda/4.8.3 requests/2.23.0 CPython/3.7.4 Linux/4.19.122-1-MANJARO manjaro/20.0.1 glibc/2.31 UID:GID : 1000:1000 netrc file : None offline mode : False ```

create new env like so:

conda create -n testgeopandas
conda activate testgeopandas
conda install -c conda-forge python=3.8 geopandas

replicate error

import geopandas

error:

ImportError: libtbb.so.2: cannot open shared object file: No such file or directory

The conda list above was after the creation of the environment as described above. geopandas import fails because of no tbb. If conda install -c conda-forge tbb then geopandas import works again.

[martinfleis]

Thank you, we are aware. That is the issue with GDAL, see the related ticket here https://github.com/conda-forge/gdal-feedstock/issues/396.

[jorisvandenbossche]

Yes, I also already noticed on GeoPandas' CI. See https://github.com/conda-forge/gdal-feedstock/issues/396

And according to chat on conda-forge gitter, this should be solved now: https://gitter.im/conda-forge/conda-forge.github.io?at=5ece403ba91f120a6cc6a98f

[jorisvandenbossche]

this should be solved now

Just waiting on the new packages to propagate to the server

[mgsnuno]

thank you for the (super) prompt response, nice. once is fixed feel free to close to issue.

[xhochy]

@mgsnuno This should be fixed, updating tiledb will resolve this in existing environments (or manually installing tbb).