Possible qiime2 conda install bug on Mac OS X

[gmdouglas (Gavin Douglas)]

Hi there,

I just ran into this error when running the default conda install commands of qiime2 on Mac 10.13.2:
NoPackagesFoundError: Packages missing in current osx-64 channels:
- intel-openmp 2018.0.0*
- libgfortran 3.0.1*
- mkl 2018.0.1*

I added “anaconda” as a channel at the top of qiime2-2017.12-py35-osx-conda.yml and this issue was resolved.

These were the commands I ran:
wget https://data.qiime2.org/distro/core/qiime2-2017.12-py35-osx-conda.yml
conda env create -n qiime2-2017.12 --file qiime2-2017.12-py35-osx-conda.yml

Thanks,

Gavin

[thermokarst]

Hi @gmdouglas - what version of conda are you running?

Can you please provide the output for conda info? I have done a few fresh installs of QIIME 2 2017.12 on macOS today, on three different machines and didn’t see this issue, for what its worth. Thanks!

[gmdouglas (Gavin Douglas)]

Hi @thermokarst, I’m running version 4.2.13. It turns out that my installation didn’t work afterall (the “qiime” binary is not found in my path after activating the environment… ). I think there is likely something wrong with my conda installation. See the conda info output below.

Thanks

              platform : osx-64
         conda version : 4.2.13
      conda is private : False
     conda-env version : 4.2.13
   conda-build version : 1.14.1
        python version : 2.7.9.final.0
      requests version : 2.8.1
      root environment : //anaconda  (writable)
   default environment : //anaconda
      envs directories : //anaconda/envs
         package cache : //anaconda/pkgs
          channel URLs : https://repo.continuum.io/pkgs/free/osx-64
                         https://repo.continuum.io/pkgs/free/noarch
                         https://repo.continuum.io/pkgs/pro/osx-64
                         https://repo.continuum.io/pkgs/pro/noarch
           config file : None
          offline mode : False

[thermokarst]

Hi @gmdouglas, at the moment we are only able to test and ensure that our environment files work with the latest conda (one of the first steps listed in the official native installation guide is to update conda). Are you able to update this deployment? Needing to add the “anaconda” channel to make things work on your machine makes sense though — more recent versions of the conda tool have changed up the default/base channels a bit. Anyway, thanks for the details and the follow-up! Please keep us posted!

[gmdouglas (Gavin Douglas)]

D’oh >.< … that was indeed the problem. I re-installed qiime2 and it’s working now. Thanks a lot for your help @thermokarst!