Incompatible packages when installing qiime2

Hi @katinker - this sounds like more of the same --- something isn't configured appropriately in your environment. The conda team put out a warning bulletin over macos catalina: Anaconda | How to Restore Anaconda after Update to MacOS Catalina . Please note, the conda team is now explicitly recommending the opposite of what @ebolyen suggested above: don't use their pkg installer, instead, use the sh installer.

As a general note, I have heard many anecdotal reports online regarding catalina breaking all kinda of things --- many software vendors are outright not supporting it. Perhaps you can save yourself some heartache and downgrade to the prior macos, and wait out the storm? I realize that is probably easier said than done.

Question - when you installed Catalina, did you do a clean sweep (delete and install), or did you perform an "upgrade" from the old macos? I have never seen the upgrade option work quite right, it is possible that there are shell/env issues there.

One bit of info that would help is if you run the env command (assuming this works at all):

env

If you get a "command not found" error again, maybe try:

bash
env

I'm still not sure I ever solved the exact problem, but I finally got qiime2 installed and (I think) working on Catalina!

I reinstalled conda via a clean sweep. Adjusting my zsh files seemed promising, but ultimately I couldn't get anything to consistently work! Finally I reverted back to bash and tried to install qiime2 via command line. I still had my original issue, where the output read:

Collecting package metadata (repodata.json): done
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes. Press CTRL-C to abort.

I never solved that problem, however once the newest qiime2 version was released (qiime2-2019.10) I was able to install it via command line with no issues.

Thank you for your patience in helping me troubleshoot this! To anyone reading...maybe wait a while before updating to Catalina.

Congratulations, sounds like an ordeal!

Does your institution have a cluster? It is also good to run it there too. Just a suggestion. Ben