Hello, I have to start working on a cluster and I tired to install Qiime2 in a conda environment, but I was reported with an error during Qiime2 installation, specifying:
Preparing transaction: done
Verifying transaction: -
SafetyError: The package for r-base located at /opt/conda/anaconda3/pkgs/r-base-4.2.2-ha7d60f8_3
appears to be corrupted. The path 'lib/R/doc/html/packages.html'
has an incorrect size.
reported size: 3423 bytes
actual size: 53278 bytes
But this does not stop the installation process, and when it has ended, I tried to test as performed in the tutorial, with:
qiime --help
And the only response I receive is this message:
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Illegal instruction
I searched for Illegal instruction issues here on the forum, but everything that was posted differs from my specific case. I wanted to run this script as indicated by @ebolyen in a closed topic, but the only response I get is:
Illegal instruction
I don't know where the issue lies and I'm asking for your help, thank you.
I found discussions about similar issues here and here. You could try to follow some of the solutions in those discussions. You might have difficulty doing so because of the permissions on your cluster, in which case you should reach out to the admins for assistance.
I've never seen this issue before so I'm not sure whether any of the above will solve your problem.
Thabk you for the quick reply!
One possible solution I'd like to try is the installation of conda on my home directory to directly manage my packages and reinstall them if any problem arises and avoiding permission issues at the same time.
I'll let you know if this helped me in resolving this problem.
Ps. One thing I dont understand is why the installation found r-base corrupted. Aren't qiime2 scripts written in python?
Unfortunately, even installing miniconda in my personal home directory inside the HPC didn't help, I made sure to unload any conda module installed on the hpc, before creating the conda environment through miniconda3 and indicating the path where I wanted the environment to be created in.
I then proceeded to install qiime2 amplicon distribution following instructions. I got the same warnings I described in the initial post.
Ps. One thing I dont understand is why the installation found r-base corrupted. Aren't qiime2 scripts written in python?
Qiime2 is written in python but various plugins use R under the hood--dada2 is an example.
I got the same warnings I described in the initial post.
I would consider reaching out to the HPC admins for help. You could also try conda config --set safety_checks disabled in your conda environment before installing, but this obviously comes with an amount of risk.
Thank you so much anyway, I contacted HPC admins for this; they tried with a precedent version of Qiime2 (2020.8 in this case) and got none of the warnings I had obtained. I might want to reinstall Qiime2 with a previous version.