title: inconsistent environment after conda updates
body: <p>Initially I wanted to install snakemake with conda.</p>
  
  <pre><code>    conda install -c bioconda -c conda-forge snakemake
  </code></pre>
  
  <p>got this </p>
  
  <pre><code>CondaValueError: Malformed version string '~': invalid character(s).
  </code></pre>
  
  <p>I found suggestions, that updating conda could help </p>
  
  <pre><code>    conda upgrade -n base conda
  </code></pre>
  
  <p>than I got this error message</p>
  
  <pre><code>The environment is inconsistent, please check the package plan carefully
  The following packages are causing the inconsistency:
  
    - conda-forge/linux-64::r-modeltools==0.2_22=r341h6115d3f_1
    - conda-forge/linux-64::r-codetools==0.2_15=r341h6115d3f_1
    - conda-forge/linux-64::r-base==3.4.1=4
    - conda-forge/linux-64::r-sandwich==2.5_0=r341h6115d3f_0
    - conda-forge/linux-64::rpy2==2.8.5=py27r3.4.1_0
    - conda-forge/linux-64::r-th.data==1.0_9=r341h6115d3f_0
    - conda-forge/linux-64::r-mvtnorm==1.0_8=r341h364d78e_0
    - bioconda/linux-64::lefse==1.0.8.post1=py27_1
    - conda-forge/linux-64::r-multcomp==1.4_8=r341h6115d3f_0
    - conda-forge/linux-64::r-zoo==1.8_3=r341hc070d10_0
    - conda-forge/linux-64::r-survival==2.42_6=r341hc070d10_1
    - conda-forge/linux-64::r-mass==7.3_50=r341hc070d10_2
    - conda-forge/linux-64::r-coin==1.2_2=r341hc070d10_0
    - defaults/linux-64::anaconda==5.1.0=py27_2
    - conda-forge/linux-64::r-matrix==1.2_14=r341hc070d10_2
    - conda-forge/linux-64::r-lattice==0.20_35=r341hc070d10_0
  </code></pre>
  
  <p>and in the end, after I tried to update anaconda, this message appeared</p>
  
  <pre><code>The environment is inconsistent, please check the package plan carefully
  The following packages are causing the inconsistency:
  
    - conda-forge/linux-64::r-modeltools==0.2_22=r341h6115d3f_1
    - defaults/linux-64::nose==1.3.7=py27heec2199_2
    - bioconda/linux-64::biom-format==2.1.7=py27_0
    - defaults/linux-64::seaborn==0.8.1=py27h633ea1e_0
    - defaults/linux-64::anaconda-navigator==1.7.0=py27_0
    - defaults/linux-64::spyder==3.2.6=py27_0
    - conda-forge/linux-64::r-codetools==0.2_15=r341h6115d3f_1
    - bioconda/linux-64::pyqi==0.3.2=py27_1
    - defaults/linux-64::anaconda-project==0.8.2=py27h236b58a_0
    - defaults/linux-64::jupyter_console==5.2.0=py27hc6bee7e_1
    - conda-forge/linux-64::r-base==3.4.1=4
    - defaults/linux-64::jupyter==1.0.0=py27_4
    - defaults/linux-64::dask==0.16.1=py27_0
    - defaults/linux-64::ipython==5.4.1=py27_2
    - defaults/linux-64::notebook==5.4.0=py27_0
    - defaults/linux-64::backports.functools_lru_cache==1.4=py27he8db605_1
    - defaults/linux-64::scikit-image==0.13.1=py27h14c3975_1
    - defaults/linux-64::numpydoc==0.7.0=py27h9647a75_0
    - defaults/linux-64::blaze==0.11.3=py27h5f341da_0
    - conda-forge/linux-64::r-sandwich==2.5_0=r341h6115d3f_0
    - conda-forge/linux-64::rpy2==2.8.5=py27r3.4.1_0
    - conda-forge/linux-64::r-th.data==1.0_9=r341h6115d3f_0
    - defaults/linux-64::isort==4.2.15=py27hcfa4749_0
    - conda-forge/linux-64::r-mvtnorm==1.0_8=r341h364d78e_0
    - defaults/linux-64::astroid==1.6.1=py27_0
    - defaults/linux-64::pyflakes==1.6.0=py27h904a57d_0
    - bioconda/linux-64::lefse==1.0.8.post1=py27_1
    - defaults/linux-64::widgetsnbextension==3.1.0=py27_0
    - defaults/linux-64::clyent==1.2.2=py27h7276e6c_1
    - defaults/linux-64::nbconvert==5.3.1=py27he041f76_0
    - conda-forge/linux-64::r-multcomp==1.4_8=r341h6115d3f_0
    - defaults/linux-64::ipykernel==4.8.0=py27_0
    - defaults/linux-64::pylint==1.8.2=py27_0
    - defaults/linux-64::ipywidgets==7.1.1=py27_0
    - defaults/linux-64::astropy==2.0.3=py27h14c3975_0
    - defaults/linux-64::jinja2==2.10=py27h4114e70_0
    - defaults/linux-64::jupyterlab_launcher==0.10.2=py27_0
    - defaults/linux-64::flask-cors==3.0.3=py27h1a8a27f_0
    - defaults/linux-64::conda-build==3.4.1=py27_0
    - defaults/linux-64::jupyterlab==0.31.5=py27_0
    - defaults/linux-64::wheel==0.30.0=py27h2bc6bb2_1
    - conda-forge/linux-64::r-zoo==1.8_3=r341hc070d10_0
    - defaults/linux-64::jsonschema==2.6.0=py27h7ed5aa4_0
    - conda-forge/linux-64::matplotlib==2.2.2=py27_1
    - conda-forge/linux-64::r-survival==2.42_6=r341hc070d10_1
    - conda-forge/linux-64::r-mass==7.3_50=r341hc070d10_2
    - conda-forge/linux-64::r-coin==1.2_2=r341hc070d10_0
    - defaults/linux-64::_ipyw_jlab_nb_ext_conf==0.1.0=py27h08a7f0c_0
    - defaults/linux-64::cython==0.27.3=py27hc56b35e_0
    - defaults/linux-64::flask==0.12.2=py27h6d5c1cd_0
    - defaults/linux-64::bleach==2.1.2=py27_0
    - defaults/linux-64::pytest==3.3.2=py27_0
    - defaults/linux-64::pygments==2.2.0=py27h4a8b6f5_0
    - defaults/linux-64::qtconsole==4.3.1=py27hc444b0d_0
    - defaults/linux-64::sphinx==1.6.6=py27_0
    - defaults/linux-64::nbformat==4.4.0=py27hed7f2b2_0
    - defaults/linux-64::odo==0.5.1=py27h9170de3_0
    - defaults/linux-64::anaconda==5.1.0=py27_2
    - defaults/linux-64::bokeh==0.12.13=py27h5233db4_0
    - conda-forge/linux-64::r-matrix==1.2_14=r341hc070d10_2
    - conda-forge/linux-64::r-lattice==0.20_35=r341hc070d10_0
    - defaults/linux-64::prompt_toolkit==1.0.15=py27h1b593e1_0
    - defaults/linux-64::anaconda-client==1.6.9=py27_0
  </code></pre>
  
  <p>And now I need help, please.
  How can this be solved without making the problem even worse (conda update --all)?</p>