Pixi error when updating 5.0.7 to 5.1.2

Install, Configure and Update
1

When we update cryosparc v5.0.7 to 5.1.2, we see this error when updating the master:

─────────────────────────────────────────────────────────────────────────────────────
Installing dependencies…
─────────────────────────────────────────────────────────────────────────────────────
Checking python dependency…
Installing python dependency…
rm: cannot remove ‘.pixi/envs/master/bin’: Directory not empty
rm: cannot remove ‘.pixi/envs/master/lib/python3.12/lib-dynload’: Directory not empty
cryosparcm ERROR: could not install python.

This can be resolved using cryosparcm deps --force, but this is not best practices.

2

Thanks for your post @davidhoover1. Is it possible that some processes related to CryoSPARC interactive jobs were still running when the software update was started? What steps did you take to ensure and confirm that no jobs were running at the time of the software update?

3

I ran a test. I installed v5.0.7 from scratch. After verifying that the server and database were running, I then ran cryosparcm update –version=5.1.2. There were no jobs running, the installation had been created less than 15 minutes prior.

1 Like
4

Also, if I update from version 4 to 5.1.2, there are no problems.

5

Thanks for providing the additional background. We are not sure what lead to the Directory not empty error. If you (or anyone else visiting this forum topic) experience this issue again, please can you run these commands and post their outputs:

ps -eo pid,ppid,start,cmd | grep -e cryosparc_ -e python -e master
cd /path/to/cryosparc_master
df -hT .
lsof .pixi/envs/master/lib/python3.12/lib-dynload # or other dir indicated in error message
ls -la pixi/envs/master/lib/python3.12/lib-dynload/