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

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
Tags:

5

Answers


  1. 0

    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.

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  2. 0

    Had the same issue with conda 4.8.2 while I tried to create an environment from a yaml file.

    loading a different, already existing environment and unloading it again did the trick in multiple occasions.

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  3. 0

    I needed to remove conda-forge from my .condarc file. Then everything worked fine.

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  4. 0

    I got this error also when trying to install a package to a personal directory on an HPC, as in:

    $ conda install -c dranew shapeit 
Solving environment: failed
CondaValueError: Malformed version string '~': invalid character(s).

    As a user of the HPC I’m not in control of the version of conda installed so had to find another solution.

    This ended up working:

    $ conda create --name shapeit -c dranew shapeit

    or in generic terms,

    $ conda create --name <packagename> -c <conda_channel_name> <packagename>

    This tells conda to create an environment named packagename, then find the package in its channel (dranew for shapeit, bioconda for OP) and install it in that new environment.

    I don’t know if it makes a difference, but I ran this code when inside my .conda/envs directory.

    Hope this helps someone else!

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  5. 0

    I had the similar problem

    conda upgrade -n base conda

    did pull the latest version but did not make the upgrade as I did not clear my previous install properly before installing latest anaconda.

    Removing /root/anaconda3 ( default installation folder in my case ) &
    removing /root/.conda & reinstalling the latest anaconda

    Post that

    conda upgrade -n base conda

    would help you upgrade to 4.16+ version ( as of today, its latest )

    One Additional Step which one must follow if they are importing env from one machine to this one:

    remove specific version from conda package dependency, example here:

    https://gitlab.com/mkuhring/TaxIt/-/commit/a8587e41bfff4c3362556c1c46d23d99ac3af069

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