Heads up for conda 4.8 and OSX 14.6

Developer Discussion
#1

Hi all –

I updated conda (incidentally because I was trying to figure out why travis tests for a plugin Im working on were failing…) and tried to install the qiime2-dev enviroment (basically v2020.06).

So, basically,

conda update conda
 wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-osx-conda.yml
conda env create -q -n test-env --file qiime2-latest-py36-osx-conda.yml

Which lead to a lovely error:

ImportError: dlopen(/Users/jusdeb/miniconda3/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so, 2): Library not loaded: @rpath/libffi.6.dylib
  Referenced from: /Users/jusdeb/miniconda3/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so
  Reason: image not found

There’s a similar github issue in the repo:

I haven’t been able to get the upgrade to work locally… but as we’re releasing 2020.6 very soon, its possibly good to be aware that (a) this may be a problem and (b) how to (possibly) troubleshoot it. I’m trying to figure out how to downgrade my conda, but at this point, people may want to be cautious about upgrades and we may want to be cautious about recommending upgrades for people in weird “No you can update your OS” limbo.

Best,
Justine

6 Likes
#2

Thank you thank you thank you @jwdebelius!

I will start looking into this, too. You’re a lifesaver!

1 Like
#3

I haven’t had time to read through that gigantic GH issue you linked to above, but, I am wondering if as a potential solution, can you (re)move the current installation, and drop a new installation in its place? That only works if your envs are in another location. For example, I install to /opt/miniconda3, and then all of my envs are in ~/.conda/envs, and the packages in ~/.conda/pkgs.

The other benefit to installing in /opt is any changes to the base env require sudo, which usually stops me from doing something on accident.

Anyway, I’ll keep looking.

3 Likes
#4

I’ll look into that! Thanks for the suggestion.

1 Like
#5

Credit goes to @ebolyen!

2 Likes