search

conda-forge / geopandas-feedstock

A conda-smithy repository for geopandas.
BSD 3-Clause "New" or "Revised" License
16 stars 14 forks source link

Cannot install geopandas in a clean environment [linux] #54

Closed hyperknot closed 5 years ago

hyperknot commented 5 years ago

I cannot install a clean geopandas environment in Linux.

A month ago, I finally figured out how to install geopandas with numexpr and bottleneck, as it was breaking a default conda + conda-forge install. The solution was to remove conda altogether and only use conda-forge. I believe setting channels to strict would have had the same effect.

You can read my issue from a month ago here: https://github.com/geopandas/geopandas/issues/924

And this is the snippet which I finally settled on:

wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh && \
    ln -s /opt/conda/bin/conda /usr/bin/conda && \
    ln -s /opt/conda/bin/python /usr/bin/condapy && \
    ln -s /opt/conda/bin/pip /usr/bin/condapip && \
    conda config --add channels conda-forge && \
    conda config --remove channels defaults && \
    conda update conda -y && \
    conda update -y --all && \
    conda install \
        geopandas numexpr bottleneck && \
    conda clean -y --all

As of today, this cannot run, as it results in a broken package solving state. Here is what the log looks like for the above command sequence.

PREFIX=/opt/conda
installing: python-3.7.1-h0371630_7 ...
Python 3.7.1
installing: ca-certificates-2018.03.07-0 ...
installing: conda-env-2.6.0-1 ...
installing: libgcc-ng-8.2.0-hdf63c60_1 ...
installing: libstdcxx-ng-8.2.0-hdf63c60_1 ...
installing: libffi-3.2.1-hd88cf55_4 ...
installing: ncurses-6.1-he6710b0_1 ...
installing: openssl-1.1.1a-h7b6447c_0 ...
installing: xz-5.2.4-h14c3975_4 ...
installing: yaml-0.1.7-had09818_2 ...
installing: zlib-1.2.11-h7b6447c_3 ...
installing: libedit-3.1.20170329-h6b74fdf_2 ...
installing: readline-7.0-h7b6447c_5 ...
installing: tk-8.6.8-hbc83047_0 ...
installing: sqlite-3.26.0-h7b6447c_0 ...
installing: asn1crypto-0.24.0-py37_0 ...
installing: certifi-2018.11.29-py37_0 ...
installing: chardet-3.0.4-py37_1 ...
installing: idna-2.8-py37_0 ...
installing: pycosat-0.6.3-py37h14c3975_0 ...
installing: pycparser-2.19-py37_0 ...
installing: pysocks-1.6.8-py37_0 ...
installing: ruamel_yaml-0.15.46-py37h14c3975_0 ...
installing: six-1.12.0-py37_0 ...
installing: cffi-1.11.5-py37he75722e_1 ...
installing: setuptools-40.6.3-py37_0 ...
installing: cryptography-2.4.2-py37h1ba5d50_0 ...
installing: wheel-0.32.3-py37_0 ...
installing: pip-18.1-py37_0 ...
installing: pyopenssl-18.0.0-py37_0 ...
installing: urllib3-1.24.1-py37_0 ...
installing: requests-2.21.0-py37_0 ...
installing: conda-4.5.12-py37_0 ...
installation finished.
Solving environment: ...working... done
urllib3-1.24.1       | 148 KB    | ########## | 100% 

pycosat-0.6.3        | 104 KB    | ########## | 100% 

asn1crypto-0.24.0    | 154 KB    | ########## | 100% 

pysocks-1.6.8        | 22 KB     | ########## | 100% 

six-1.12.0           | 22 KB     | ########## | 100% 

chardet-3.0.4        | 167 KB    | ########## | 100% 

ruamel_yaml-0.15.71  | 256 KB    | ########## | 100% 

yaml-0.1.7           | 78 KB     | ########## | 100% 

pyopenssl-19.0.0     | 81 KB     | ########## | 100% 

libffi-3.2.1         | 46 KB     | ########## | 100% 

certifi-2019.3.9     | 149 KB    | ########## | 100% 

conda-4.6.8          | 872 KB    | ########## | 100% 

openssl-1.1.1b       | 4.0 MB    | ########## | 100% 

pycparser-2.19       | 171 KB    | ########## | 100% 

requests-2.21.0      | 84 KB     | ########## | 100% 

ca-certificates-2019 | 146 KB    | ########## | 100% 

cryptography-2.6.1   | 607 KB    | ########## | 100% 

cffi-1.12.2          | 218 KB    | ########## | 100% 

idna-2.8             | 100 KB    | ########## | 100% 
## Package Plan ##

  environment location: /opt/conda

  added / updated specs: 
    - conda

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    urllib3-1.24.1             |        py37_1000         148 KB  conda-forge
    pycosat-0.6.3              |py37h14c3975_1001         104 KB  conda-forge
    asn1crypto-0.24.0          |        py37_1003         154 KB  conda-forge
    pysocks-1.6.8              |        py37_1002          22 KB  conda-forge
    six-1.12.0                 |        py37_1000          22 KB  conda-forge
    chardet-3.0.4              |        py37_1003         167 KB  conda-forge
    ruamel_yaml-0.15.71        |py37h14c3975_1000         256 KB  conda-forge
    yaml-0.1.7                 |    h14c3975_1001          78 KB  conda-forge
    pyopenssl-19.0.0           |           py37_0          81 KB  conda-forge
    libffi-3.2.1               |    he1b5a44_1006          46 KB  conda-forge
    certifi-2019.3.9           |           py37_0         149 KB  conda-forge
    conda-4.6.8                |           py37_0         872 KB  conda-forge
    openssl-1.1.1b             |       h14c3975_1         4.0 MB  conda-forge
    pycparser-2.19             |           py37_1         171 KB  conda-forge
    requests-2.21.0            |        py37_1000          84 KB  conda-forge
    ca-certificates-2019.3.9   |       hecc5488_0         146 KB  conda-forge
    cryptography-2.6.1         |   py37h72c5cf5_0         607 KB  conda-forge
    cffi-1.12.2                |   py37hf0e25f4_1         218 KB  conda-forge
    idna-2.8                   |        py37_1000         100 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         7.3 MB

The following packages will be UPDATED:

    asn1crypto:      0.24.0-py37_0          --> 0.24.0-py37_1003          conda-forge
    ca-certificates: 2018.03.07-0           --> 2019.3.9-hecc5488_0       conda-forge
    certifi:         2018.11.29-py37_0      --> 2019.3.9-py37_0           conda-forge
    cffi:            1.11.5-py37he75722e_1  --> 1.12.2-py37hf0e25f4_1     conda-forge
    chardet:         3.0.4-py37_1           --> 3.0.4-py37_1003           conda-forge
    conda:           4.5.12-py37_0          --> 4.6.8-py37_0              conda-forge
    cryptography:    2.4.2-py37h1ba5d50_0   --> 2.6.1-py37h72c5cf5_0      conda-forge
    idna:            2.8-py37_0             --> 2.8-py37_1000             conda-forge
    libffi:          3.2.1-hd88cf55_4       --> 3.2.1-he1b5a44_1006       conda-forge
    openssl:         1.1.1a-h7b6447c_0      --> 1.1.1b-h14c3975_1         conda-forge
    pycosat:         0.6.3-py37h14c3975_0   --> 0.6.3-py37h14c3975_1001   conda-forge
    pycparser:       2.19-py37_0            --> 2.19-py37_1               conda-forge
    pyopenssl:       18.0.0-py37_0          --> 19.0.0-py37_0             conda-forge
    pysocks:         1.6.8-py37_0           --> 1.6.8-py37_1002           conda-forge
    requests:        2.21.0-py37_0          --> 2.21.0-py37_1000          conda-forge
    ruamel_yaml:     0.15.46-py37h14c3975_0 --> 0.15.71-py37h14c3975_1000 conda-forge
    six:             1.12.0-py37_0          --> 1.12.0-py37_1000          conda-forge
    urllib3:         1.24.1-py37_0          --> 1.24.1-py37_1000          conda-forge
    yaml:            0.1.7-had09818_2       --> 0.1.7-h14c3975_1001       conda-forge

Downloading and Extracting Packages
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done

Collecting package metadata: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /opt/conda

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.6                |    h14c3975_1002         415 KB  conda-forge
    conda-env-2.6.0            |                1           2 KB  conda-forge
    libedit-3.1.20170329       |    hf8c457e_1001         172 KB  conda-forge
    ncurses-6.1                |    hf484d3e_1002         1.3 MB  conda-forge
    pip-19.0.3                 |           py37_0         1.8 MB  conda-forge
    python-3.7.3               |       h5b0a415_0        35.7 MB  conda-forge
    readline-7.0               |    hf8c457e_1001         391 KB  conda-forge
    setuptools-40.8.0          |           py37_0         625 KB  conda-forge
    sqlite-3.26.0              |    h67949de_1001         1.9 MB  conda-forge
    tk-8.6.9                   |    h84994c4_1001         3.2 MB  conda-forge
    wheel-0.33.1               |           py37_0          34 KB  conda-forge
    xz-5.2.4                   |    h14c3975_1001         366 KB  conda-forge
    zlib-1.2.11                |    h14c3975_1004         101 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        46.0 MB

The following NEW packages will be INSTALLED:

  bzip2              conda-forge/linux-64::bzip2-1.0.6-h14c3975_1002

The following packages will be UPDATED:

  libedit            pkgs/main::libedit-3.1.20170329-h6b74~ --> conda-forge::libedit-3.1.20170329-hf8c457e_1001
  ncurses                 pkgs/main::ncurses-6.1-he6710b0_1 --> conda-forge::ncurses-6.1-hf484d3e_1002
  pip                            pkgs/main::pip-18.1-py37_0 --> conda-forge::pip-19.0.3-py37_0
  python                 pkgs/main::python-3.7.1-h0371630_7 --> conda-forge::python-3.7.3-h5b0a415_0
  readline               pkgs/main::readline-7.0-h7b6447c_5 --> conda-forge::readline-7.0-hf8c457e_1001
  setuptools            pkgs/main::setuptools-40.6.3-py37_0 --> conda-forge::setuptools-40.8.0-py37_0
  sqlite                pkgs/main::sqlite-3.26.0-h7b6447c_0 --> conda-forge::sqlite-3.26.0-h67949de_1001
  tk                         pkgs/main::tk-8.6.8-hbc83047_0 --> conda-forge::tk-8.6.9-h84994c4_1001
  wheel                      pkgs/main::wheel-0.32.3-py37_0 --> conda-forge::wheel-0.33.1-py37_0
  xz                         pkgs/main::xz-5.2.4-h14c3975_4 --> conda-forge::xz-5.2.4-h14c3975_1001
  zlib                    pkgs/main::zlib-1.2.11-h7b6447c_3 --> conda-forge::zlib-1.2.11-h14c3975_1004

The following packages will be SUPERSEDED by a higher-priority channel:

  conda-env                              pkgs/main/linux-64 --> conda-forge/noarch

Downloading and Extracting Packages

bzip2-1.0.6          | 415 KB    | ########## | 100% 

sqlite-3.26.0        | 1.9 MB    | ########## | 100% 

libedit-3.1.20170329 | 172 KB    | ########## | 100% 

zlib-1.2.11          | 101 KB    | ########## | 100% 

pip-19.0.3           | 1.8 MB    | ########## | 100% 

python-3.7.3         | 35.7 MB   | ########## | 100% 

tk-8.6.9             | 3.2 MB    | ########## | 100% 

wheel-0.33.1         | 34 KB     | ########## | 100% 

ncurses-6.1          | 1.3 MB    | ########## | 100% 

setuptools-40.8.0    | 625 KB    | ########## | 100% 

readline-7.0         | 391 KB    | ########## | 100% 

conda-env-2.6.0      | 2 KB      | ########## | 100% 

xz-5.2.4             | 366 KB    | ########## | 100% 
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata: ...working... done
Solving environment: ...working... failed

PackagesNotFoundError: The following packages are not available from current channels:

  - geopandas -> fiona -> gdal[version='>=2.4.1,<2.5.0a0'] -> libgdal==2.4.1=hdb8f723_0 -> hdf5[version='>=1.10.4,<1.10.5.0a0'] -> libgfortran-ng[version='>=7,<8.0a0']
  - geopandas -> fiona -> gdal[version='>=2.4.1,<2.5.0a0'] -> libgdal==2.4.1=hdb8f723_0 -> libnetcdf[version='>=4.6.2,<4.6.3.0a0']

Current channels:

  - https://conda.anaconda.org/conda-forge/linux-64
  - https://conda.anaconda.org/conda-forge/noarch

Were there any recent updates which broke this? How can I possibly fix this?

hyperknot commented 5 years ago

This is solved and documented in https://github.com/geopandas/geopandas/issues/924