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Docker Build Failure #73

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strixcuriosus opened this issue Apr 16, 2019 · 5 comments
Closed

Docker Build Failure #73

strixcuriosus opened this issue Apr 16, 2019 · 5 comments

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@strixcuriosus
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The docker build is failing on the conda install:

Sending build context to Docker daemon   5.12kB
Step 1/12 : FROM jupyter/minimal-notebook:2c80cf3537ca
 ---> db464e6587fb
Step 2/12 : RUN conda install -y -c conda-forge gdal=2.4.0
 ---> Running in 2a389bdcb711
Fetching package metadata ...An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

    https://github.com/conda/conda/issues



Current conda install:

               platform : linux-64
          conda version : 4.3.29
       conda is private : False
      conda-env version : 4.3.29
    conda-build version : not installed
         python version : 3.6.3.final.0
       requests version : 2.18.4
       root environment : /opt/conda  (writable)
    default environment : /opt/conda
       envs directories : /opt/conda/envs
                          /home/jovyan/.conda/envs
          package cache : /opt/conda/pkgs
                          /home/jovyan/.conda/pkgs
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : /opt/conda/.condarc
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.29 requests/2.18.4 CPython/3.6.3 Linux/4.9.125-linuxkit debian/stretch/sid glibc/2.23
                UID:GID : 1000:100

`$ /opt/conda/bin/conda install -y -c conda-forge gdal=2.4.0`




    Traceback (most recent call last):
      File "/opt/conda/lib/python3.6/site-packages/conda/exceptions.py", line 640, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 140, in _main
        exit_code = args.func(args, p)
      File "/opt/conda/lib/python3.6/site-packages/conda/cli/main_install.py", line 80, in execute
        install(args, parser, 'install')
      File "/opt/conda/lib/python3.6/site-packages/conda/cli/install.py", line 231, in install
        unknown=index_args['unknown'], prefix=prefix)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/index.py", line 101, in get_index
        index = fetch_index(channel_priority_map, use_cache=use_cache)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/index.py", line 120, in fetch_index
        repodatas = collect_all_repodata(use_cache, tasks)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 75, in collect_all_repodata
        repodatas = _collect_repodatas_serial(use_cache, tasks)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 485, in _collect_repodatas_serial
        for url, schan, pri in tasks]
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 485, in <listcomp>
        for url, schan, pri in tasks]
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 115, in func
        res = f(*args, **kwargs)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 473, in fetch_repodata
        with open(cache_path, 'w') as fo:
    FileNotFoundError: [Errno 2] No such file or directory: '/opt/conda/pkgs/cache/497deca9.json'

The command '/bin/sh -c conda install -y -c conda-forge gdal=2.4.0' returned a non-zero code: 1

This looks closely related to the recent gdal version issue mentioned in #71
which inspired the upgrade of gdal in
#72
@strixcuriosus
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for debugging purposes, the install issue can be reproduced in a jupyter/minimal-notebook:2c80cf3537ca container like so:

docker run --rm -it jupyter/minimal-notebook:2c80cf3537ca  /bin/bash
jovyan@c783b1710647:~$
jovyan@c783b1710647:~$  conda install -y -c conda-forge gdal=2.4.0
Fetching package metadata ...An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:

    https://github.com/conda/conda/issues



Current conda install:

               platform : linux-64
          conda version : 4.3.29
       conda is private : False
      conda-env version : 4.3.29
    conda-build version : not installed
         python version : 3.6.3.final.0
       requests version : 2.18.4
       root environment : /opt/conda  (writable)
    default environment : /opt/conda
       envs directories : /opt/conda/envs
                          /home/jovyan/.conda/envs
          package cache : /opt/conda/pkgs
                          /home/jovyan/.conda/pkgs
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.continuum.io/pkgs/main/linux-64
                          https://repo.continuum.io/pkgs/main/noarch
                          https://repo.continuum.io/pkgs/free/linux-64
                          https://repo.continuum.io/pkgs/free/noarch
                          https://repo.continuum.io/pkgs/r/linux-64
                          https://repo.continuum.io/pkgs/r/noarch
                          https://repo.continuum.io/pkgs/pro/linux-64
                          https://repo.continuum.io/pkgs/pro/noarch
            config file : /opt/conda/.condarc
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.29 requests/2.18.4 CPython/3.6.3 Linux/4.9.125-linuxkit debian/stretch/sid glibc/2.23
                UID:GID : 1000:100

`$ /opt/conda/bin/conda install -y -c conda-forge gdal=2.4.0`




    Traceback (most recent call last):
      File "/opt/conda/lib/python3.6/site-packages/conda/exceptions.py", line 640, in conda_exception_handler
        return_value = func(*args, **kwargs)
      File "/opt/conda/lib/python3.6/site-packages/conda/cli/main.py", line 140, in _main
        exit_code = args.func(args, p)
      File "/opt/conda/lib/python3.6/site-packages/conda/cli/main_install.py", line 80, in execute
        install(args, parser, 'install')
      File "/opt/conda/lib/python3.6/site-packages/conda/cli/install.py", line 231, in install
        unknown=index_args['unknown'], prefix=prefix)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/index.py", line 101, in get_index
        index = fetch_index(channel_priority_map, use_cache=use_cache)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/index.py", line 120, in fetch_index
        repodatas = collect_all_repodata(use_cache, tasks)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 75, in collect_all_repodata
        repodatas = _collect_repodatas_serial(use_cache, tasks)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 485, in _collect_repodatas_serial
        for url, schan, pri in tasks]
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 485, in <listcomp>
        for url, schan, pri in tasks]
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 115, in func
        res = f(*args, **kwargs)
      File "/opt/conda/lib/python3.6/site-packages/conda/core/repodata.py", line 473, in fetch_repodata
        with open(cache_path, 'w') as fo:
    FileNotFoundError: [Errno 2] No such file or directory: '/opt/conda/pkgs/cache/497deca9.json'

@sarasafavi
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For an undetermined reason, older tags of the minimal-notebook image appear to throw this error. Workaround for now is to remove your local instance of that image and then re-build Notebooks; e.g.,

$ docker images
<take note of the ID for jupyter/minimal-notebook>
$ docker rmi <ID noted above>
$ docker build --rm -t planet-notebooks .

A longer-term fix is that we use our own docker image; I'll create a new issue for that.

@sarasafavi sarasafavi mentioned this issue Apr 16, 2019
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@strixcuriosus
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Thanks for the suggestion @sarasafavi!
I was able to get a successful build after removing the jupyter/minimal-notebook image and cache layers. I took the rather zealous approach of doing a docker image prune -a

@manivasaganrama
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manivasaganrama commented Aug 7, 2019 •
edited
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When I am trying to execute this command in terminal:

@sarasafavi
@jreiberkyle
@danabauer
@nateweisiger
@MattFerraro
@theTechie
@geowurster
@spencermathews
@jakedahn
@gitter-badger

docker rmi

I am getting:

Error response from daemon: conflict: unable to delete db464e6587fb (must be forced) - image is being used by stopped container 048ff8c32674

Need help

@strixcuriosus
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Contributor Author

For anyone else who hits the problem @manivasaganrama found, you can remove containers with docker rm
https://docs.docker.com/engine/reference/commandline/rm/#remove-all-stopped-containers
e.g. docker rm 048ff8c32674

You may also find docker system prune to be helpful
https://docs.docker.com/engine/reference/commandline/system_prune/

@strixcuriosus strixcuriosus mentioned this issue Sep 26, 2019
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3 participants
@sarasafavi @strixcuriosus @manivasaganrama