I'm trying to install qiime2-2023.5 using these instructions. I already have miniconda3 installed so that's the only part of the instructions I didn't follow. Otherwise, I updated my conda, wget'ed the yml file and ran conda env create -n qiime2-2023.5 --file qiime2-2023.5-py38-linux-conda.yml to install qiime2. But I am getting the following errors. Judging by what they say, I don't think it's a big deal but the installation is stuck at the Executing transaction: / step.
[ taruna@knot] ~
$ conda env create -n qiime2-2023.5 --file qiime2-2023.5-py38-linux-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: done
Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: \
SafetyError: The package for platformdirs located at /home/taruna/miniconda3/pkgs/platformdirs-3.5.1-pyhd8ed1ab_0
appears to be corrupted. The path 'site-packages/platformdirs-3.5.1.dist-info/licenses/LICENSE'
has an incorrect size.
reported size: 1089 bytes
actual size: 0 bytes
SafetyError: The package for platformdirs located at /home/taruna/miniconda3/pkgs/platformdirs-3.5.1-pyhd8ed1ab_0
appears to be corrupted. The path 'site-packages/platformdirs/macos.py'
has an incorrect size.
reported size: 3329 bytes
actual size: 0 bytes
SafetyError: The package for platformdirs located at /home/taruna/miniconda3/pkgs/platformdirs-3.5.1-pyhd8ed1ab_0
appears to be corrupted. The path 'site-packages/platformdirs/windows.py'
has an incorrect size.
reported size: 8612 bytes
actual size: 0 bytes
done
Executing transaction: /
Please advise. Thank you very much for your help in advance!
Thanks for reaching out! These SafetyError messages typically pop up when you have existing packages on your machine that are competing with the package versions included in your installation of QIIME 2. It is interesting that the actual size for these packages are 0 bytes though.
Can you run the following commands and provide the output(s) in your response:
Hello @lizgehret - sorry for the delay in responding. I was working on a different project so I couldn't finish Qiime2 install. But here are the results from the commands you asked me to run.
it looks like there were some issues downloading packages from conda, or the operation was interrupted. Now conda wants to use cache all the time, but it's corrupted. To fix it:
Hi @crusher083 - thank you for your suggestions. I tried those commands, however, now I'm getting a core dumped error.
$ qiime --help
QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Illegal instruction (core dumped)
Thank you very much, @crusher083! Fortunately I have access to another cluster on which I was able to install Qiime2 without issues. I will read through the thread you shared. Thank you for sharing!
