Problem upgrading to 2017.6

[Scott_Kelley]

I tried to update my qiime2 distribution to the latest and ran into big trouble.

[Platform: macOS Sierra 10.12.5]

First, I updated conda, which appears to work, then I ran:

conda install --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-osx-64.txt

But then this happened:

CondaError: CondaHTTPError: HTTP None None for url <https://repo.continuum.io/pkgs/r/osx-64/r-stringi-1.1.1-r3.3.1_0.tar.bz2>**

I tried rerunning the conda install command, and it seemed to work and finish, but then I tried:

Varykinas-MacBook-Pro:~ kina$ source activate qiime2-2017.6
Traceback (most recent call last):
File "/Users/kina/anaconda/bin/conda", line 4, in <module>
    import conda.cli
ImportError: No module named 'conda'

Conda is no longer working. I’ve put in the output below.

Anyone know what might have happened or how to fix it?

Thanks! -Scott

Here are the commands and output:

Varykinas-MacBook-Pro:~ kina$ conda update conda
Fetching package metadata .........
Solving package specifications: .

Package plan for installation in environment /Users/kina/anaconda:

The following packages will be UPDATED:

    conda: 4.3.18-py36_0 --> 4.3.22-py36_0

Proceed ([y]/n)? y

conda-4.3.22-p 100% |################################| Time: 0:00:00 735.55 kB/s
Varykinas-MacBook-Pro:~ kina$ source activate qiime2-2017.6

CondaEnvironmentNotFoundError: Could not find environment: qiime2-2017.6 .
You can list all discoverable environments with `conda info --envs`.

Varykinas-MacBook-Pro:~ kina$ conda install --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-osx-64.txt
bioconductor-b 100% |################################| Time: 0:00:02 937.93 kB/s
bioconductor-b 100% |################################| Time: 0:00:00 805.50 kB/s
bioconductor-b 100% |################################| Time: 0:00:00 896.90 kB/s
bioconductor-b 100% |################################| Time: 0:00:15 913.41 kB/s
bioconductor-d 100% |################################| Time: 0:00:02 670.62 kB/s
bioconductor-g 100% |################################| Time: 0:00:14   1.02 MB/s
..etc.

CondaError: CondaHTTPError: HTTP None None for url <https://repo.continuum.io/pkgs/r/osx-64/r-stringi-1.1.1-r3.3.1_0.tar.bz2>
Elapsed: None

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

Varykinas-MacBook-Pro:~ kina$ conda install --file https://data.qiime2.org/distro/core/qiime2-2017.6-conda-osx-64.txt
r-stringi-1.1. 100% |################################| Time: 0:00:07   1.48 MB/s
r-stringr-1.0. 100% |################################| Time: 0:00:00   2.28 MB/s
r-survival-2.3 100% |################################| Time: 0:00:06 694.54 kB/s
requests-2.14. 100% |################################| Time: 0:00:01 377.52 kB/s
scikit-bio-0.5 100% |################################| Time: 0:00:04 270.70 kB/s
scikit-learn-0 100% |################################| Time: 0:00:13 382.86 kB/s
scipy-0.19.0-n 100% |################################| Time: 0:00:30 510.13 kB/s
sortmerna-2.0- 100% |################################| Time: 0:00:01 218.78 kB/s
statsmodels-0. 100% |################################| Time: 0:00:07 899.20 kB/s
terminado-0.6- 100% |################################| Time: 0:00:00   1.61 MB/s
testpath-0.3.1 100% |################################| Time: 0:00:00 698.06 kB/s
tornado-4.5.1- 100% |################################| Time: 0:00:00   1.02 MB/s
tzlocal-1.3-py 100% |################################| Time: 0:00:00 202.99 kB/s
vsearch-2.0.3- 100% |################################| Time: 0:00:00 234.03 kB/s
widgetsnbexten 100% |################################| Time: 0:00:01 718.31 kB/s
Varykinas-MacBook-Pro:~ kina$ source activate qiime2-2017.6
Traceback (most recent call last):
  File "/Users/kina/anaconda/bin/conda", line 4, in <module>
    import conda.cli
ImportError: No module named 'conda'

[jairideout (Jai Ram Rideout)]

Hi @Scott_Kelley! It looks like you accidentally installed QIIME 2 into your root conda environment. Using conda install --file ... will install QIIME 2 into your current environment, which happened to be your root environment. The QIIME 2 install docs recommend using conda create instead of conda install so that a new QIIME 2 environment is created that is separate from your root environment.

It appears that your root environment is now broken. If you aren’t too attached to your Anaconda (or Miniconda) installation you could try deleting it (you’ll lose all your conda environments) and reinstalling Anaconda or Miniconda. That is likely the easiest path forward.

If you’d like to avoid reinstalling Anaconda/Miniconda we can try to fix your root environment. I’ll need the output from the following commands:

1. Open a new terminal.
2. Run conda update conda (hopefully this just works)
3. which conda
4. which python
5. python --version
6. conda list
7. echo $PATH
8. echo $PYTHONPATH
9. echo $PYTHONHOME