CondaValueError: Malformed version string '~': invalid character(s)

Question

I'm getting a Malformed version string error with my conda. I have no idea how to debug this or how to check it.

Can anyone help? GitHub has talked about the issue but I haven't seen any fixes.

-bash-4.1$ conda install -c bioconda pysam
Solving environment: failed



 1. CondaValueError: Malformed version string '~': invalid character(s).

In response to the comment below:

(mage_env) -bash-4.1$ echo $PATH
/usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/mage_env/bin:/usr/local/packages/jdk-8u121/bin/:/usr/local/bin:/usr/local/devel/ANNOTATION/rrichter/local/bin:/home/syooseph/utils/clustalw1.83:/usr/local/packages/gsl/bin:/usr/local/sge_current/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/devel/ANNOTATION/jespinoz/anaconda/bin:/usr/local/devel/ANNOTATION/jespinoz/Dropseq/:/usr/local/devel/ANNOTATION/jespinoz/Dropseq/Drop-seq_tools-1.13/
(mage_env) -bash-4.1$ conda info

     active environment : mage_env
    active env location : /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs/mage_env
            shell level : 1
       user config file : /home/jespinoz/.condarc
 populated config files : /home/jespinoz/.condarc
          conda version : 4.5.11
    conda-build version : not installed
         python version : 3.6.2.final.0
       base environment : /usr/local/devel/ANNOTATION/jespinoz/anaconda  (writable)
           channel URLs : https://conda.anaconda.org/ursky/linux-64
                          https://conda.anaconda.org/ursky/noarch
                          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.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
                          https://repo.anaconda.com/pkgs/pro/linux-64
                          https://repo.anaconda.com/pkgs/pro/noarch
          package cache : /usr/local/devel/ANNOTATION/jespinoz/anaconda/pkgs
                          /home/jespinoz/.conda/pkgs
       envs directories : /usr/local/devel/ANNOTATION/jespinoz/anaconda/envs
                          /home/jespinoz/.conda/envs
               platform : linux-64
             user-agent : conda/4.5.11 requests/2.14.2 CPython/3.6.2 Linux/2.6.32-696.18.7.el6.x86_64 centos/6.4 glibc/2.12
                UID:GID : 3456:63
             netrc file : None
           offline mode : False

Answer 1

This looks like it was fixed with Conda 4.6.0. Upgrading your Conda should resolve the issue.

conda upgrade -n base conda

If you have trouble solving environment, I suggest trying

conda upgrade -n base -c defaults --override-channels conda

This will exclude all other channels during the solving process, and helps because having too many options to prune is one of the main reasons for slow solves.