install qiime2-2023.2 errors on M1 after following all instructions

Technical Support
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I have been trying to install the new version of qiime2 for the past couple of days and have tried the tips from this forum with no solution. I have used the qiime2-2022.11 and 2022.8 version successfully with no install problems so I am not sure what is happening.

I specifically followed this post as I am using an M1 mac Install QIIME2 on Macbook Pro 2021 with apple M1 Chip which ran the "Found conflicts! Looking for incompatible packages." much faster (1hr vs 4+ hrs) than any of the other instructions I tried.

It resulted in over 20,000 lines of error so I won't copy and paste but maybe this file will work:
qiime2installerrors.txt (2.3 MB)

I did update conda before doing the install of qiime2. I have also tried completely removing miniconda3 several times and re-installing it before I switched to miniforge3. I also tried removing miniforge3 and re-installing. I am using terminal with rosetta2.

Can anyone provide some help?

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Hi @jdv,

Welcome to the :qiime2: forum!

Sorry to hear about your difficulties installing QIIME 2!

Let's have you try a couple of things:

  1. Try using the install instructions for macOS (Intel) and OS X and see if that is successful.
  2. Try running conda clean --all before attempting to re-install.

If neither of these work, can you provide the output from your terminal after running conda env list?

Cheers :lizard:

1 Like
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Hello! I did steps 1 and 2, it ran for about 3 hrs and did not install.

Here is the output for conda env list

conda environments:

base /Users/jessicadiaz/miniconda3

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Hello @jdv,

I have an m1 MacBook, and have a working installation of 2023.2. I had some problems previously with a miniconda installation :snake::microscope:, and replaced that with anaconda :snake:.

If you have the space and don't mind getting rid of your miniconda installation, you could try this. I followed the the standard Mac installation instructions (the "macOS (Intel) and OS X" tab here).

Hope this works for you.

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Thank you for the suggestion! Did you install anaconda with the rosetta2 activated?

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Hey @jdv,

I had the same struggle with updating from qiime2-2022.11 to 2022.8 on my Macbook Pro 2021 M1 :upside_down_face:. After updating conda I wasn't even able to run "conda info". I deactivated/deleted conda and any other qiime2 folder/info on my lapotop. Afterwards I restarted my macbook, installed miniconda and qiime2-2023.2 following the instructions and it worked. Make sure rosetta2 is activated :slight_smile:
Check out this link: Install QIIME2 on Macbook Pro 2021 with apple M1 Chip; maybe it can help you.
I really hope this helps! :hugs:

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@aliral Thank you! :slight_smile: This worked for my current user profile, I had to delete everything and restart. I installed anaconda instead of miniconda.

Before this solution, I also created a new user on my mac with admin privileges and only installed anaconda and qiime2 and that ran successfully. I think I'll keep working out of the new user for all my terminal & qiime2 needs just to be on the safe side that other apps are not interfering. It seemed that having R installed as an app (for Rstudio) was causing issues due to different versions of R with conda?

Thanks everyone for the quick help!!

1 Like
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@jdv,

Glad you were able to get things working!

Yes, this can definitely happen if you have separate R instances installed - those can compete within conda, causing conflicts that don't exist in the environment itself.

For utilizing R separately from QIIME 2, I prefer to create a specific conda environment with R installed - this helps to keep things separate and prevents conflicts such as what you ran into above.

Cheers :lizard:

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