Illegal instruction(core dumped) after development

Hi @lizgehret and @ebolyen

I have worked on an issue with q2 composition da-barplot and it seems that some of my 'actions' did affect the miniconda environment. I cannot run 'q2 dev refresh-cache' but get stacked at the 'illegal instruction (core dumped)' (in German 'Ungültiger Maschinenbefehl (Speicherabzug geschrieben)'.

I have re-installed the conda environment and subsequently also miniconda, but it did not resolve this issue.
The same happens when installing the 12-2022.11 conda environment.

My computer is running on AlmaLinux9 with the Miniconda3 / Python 3.9. (I have also tested Miniconda / Python 3.8, same issue).

Has anybody observed this with miniconda?
Fortunately, this issue occured on my test server, where I try to fix the da-barplot issue, a separate productive server (Almalinux 9 and Miniconda3/Python 3.8) is fine with qiime2-2023.2.

Best regards

Hi @arwqiime,
It sounds like the changes you made to the q2 composition da-barplot might be causing this issue? Do you have a PR that I could review to see if I see anything?

It sounds like it's related to this issue a few other folks are having:

@arwqiime we don't have a good solution at the moment, but we're collecting info in that thread.

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Hi @cherman2
My previous post was misleading, sorry. You wrote in the other post that the da-barplot issue seems to be related to the python dependency 'altair', which I have not yet addressed.
The 'action' menitioned above could be to the installation of the q2-motus third party plugin, which I had installed before. I used mamba here (as recommended), and I cannot rule out that mamba created the problems here. At least the illegal instructions issue started around this action.
This could be just a coincidence, as the new miniconda installation does not have mamba, but the issue persists.
I don't know if mamba installer add something outside miniconda.
I will see if @ebolyen will find out some more details and I will then try to fix it on my test server, before touching my productive server which works fine with q2-2023.2 at the moment.

Best regards

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That sounds like a good plan to me! Thanks @ebolyen for the info!

Hi @cherman2 @ebolyen
I could finally get the illegal instruction issue fixed using the workaurond posted on QIIME is caching your current deployment.....Illegal instruction (core dumped) - #71.
However, there seem to be other issues introduced here, and q2 composition ancombc now showed an R related error.
However, this was done on my older HPE server (DL180 G6 which I use for testing).

Therefore I used a newer servers showing the da_barplot issue with altair v. 3.1.0. After updating to altair=4.2.2, the da_barplot issue is gone. And it seems that installing q2-2023.2 now also installs altair=4.2.2, which was not the case last February.

Thank you for your support!

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