Conda freezes at 'Solving package specifications' during installation

[Former user]

Hi there. Thanks for developing this excellent tool.

After re-imaging my machine I find that conda freezes at 'Solving package specifications' when re-installing mageck-vispr.

Current conda install:

           platform : osx-64
      conda version : 4.3.29
   conda is private : False
  conda-env version : 4.3.29
conda-build version : not installed
     python version : 3.6.1.final.0
   requests version : 2.14.2
   root environment : /Users/analysis/miniconda3  (writable)
default environment : /Users/analysis/miniconda3
   envs directories : /Users/analysis/miniconda3/envs
                      /Users/analysis/.conda/envs
      package cache : /Users/analysis/miniconda3/pkgs
                      /Users/analysis/.conda/pkgs
       channel URLs : https://conda.anaconda.org/bioconda/osx-64
                      https://conda.anaconda.org/bioconda/noarch
                      https://conda.anaconda.org/conda-forge/osx-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://repo.continuum.io/pkgs/main/osx-64
                      https://repo.continuum.io/pkgs/main/noarch
                      https://repo.continuum.io/pkgs/free/osx-64
                      https://repo.continuum.io/pkgs/free/noarch
                      https://repo.continuum.io/pkgs/r/osx-64
                      https://repo.continuum.io/pkgs/r/noarch
                      https://repo.continuum.io/pkgs/pro/osx-64
                      https://repo.continuum.io/pkgs/pro/noarch
                      https://conda.anaconda.org/r/osx-64
                      https://conda.anaconda.org/r/noarch
        config file : /Users/analysis/.condarc
         netrc file : None
       offline mode : False
         user-agent : conda/4.3.29 requests/2.14.2 CPython/3.6.1 Darwin/16.7.0 OSX/10.12.6    
            UID:GID : 502:20

[Lai Wei]

You may need to add several channels using the following code:

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

[Paul Datlinger]

Hello. Did anyone manage to solve this issue? I'm using Miniconda3 based on Python 3.6 and I configured it to use the Bioconda channels, as described in your tutorial. Then I'm trying to install in a new environment by:

conda create -n mageck-vispr mageck-vispr

However, Miniconda3 always gets stuck at "Solving package specifications: ." for > 10 min.

I'd be really grateful if you have any suggestions.

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 : /home/pdatlinger/tools/miniconda3  (writable)
    default environment : /home/pdatlinger/tools/miniconda3
       envs directories : /home/pdatlinger/tools/miniconda3/envs
                          /home/pdatlinger/.conda/envs
          package cache : /home/pdatlinger/tools/miniconda3/pkgs
                          /home/pdatlinger/.conda/pkgs
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          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
                          https://conda.anaconda.org/r/linux-64
                          https://conda.anaconda.org/r/noarch
            config file : /home/pdatlinger/.condarc
             netrc file : None
           offline mode : False
             user-agent : conda/4.3.29 requests/2.18.4 CPython/3.6.3 Linux/2.6.32-431.20.3.el6.x86_64 Scientific Linux/6.5 glibc/2.12    
                UID:GID : 10120:20024

All the best, Paul

[Wei Li]

This seems to be an issue in conda. It seems that they are still working on solving this bug (see the discussion here).

[Wei Li]

Based on their discussion, the best way is to remove r channel from conda (although it does not guarantee to solve the problem). Follow the instruction here.

[Wei Li]

I tested it just now and it works by removing the r channel. So it's closed but let me know if there are still further problems.

[Michael Apostolides]

Hello Wei Li, I tried to follow the instructions at the link you provided, but could not figure it out. It still hangs and I'm unable to install the environment to work with mageck-vispr

[TB]

I also encountered the the same problem. I found a way to work around this

conda create -n  mageck-vispr bismark
source activate  mageck-vispr
conda install  mageck-vispr

Now you can use mageck-vispr. I'm not sure about the reason. But it works for me.