Failure to Verify when reinstalling updated version of QIIME2

I am trying to install an updated version of QIIME2 on a departmental computer. I first ran into some problems with permissions, but once an override code was identified I am now getting an unfamiliar error response during the final stage of installation. Wget is working find from what I can tell, but when I create the new conda environment it gives my the error code below during the verification step and stops the installation. A new qiime directory is created in the envs folder, but it only has an empty conda-meta directory.

Some troubleshooting I have done so far that has been unsuccessful:

  • updated miniconda to newest version 23.9.0
  • conda clean --all

I am at a loss so any advise would be greatly appreciated. Thank you in advance!

Input: conda env create -n qiime2-2023.7 --file qiime2-2023.7-py38-osx-conda.yml
Output: Collecting package metadata (repodata.json): done
Solving environment: done

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: failed

CondaVerificationError: The package for expat located at /usr/local/bin/miniconda/pkgs/expat-2.5.0-hf0c8a7f_1
appears to be corrupted. The path 'lib/libexpat.dylib'
specified in the package manifest cannot be found.

CondaVerificationError: The package for gsl located at /usr/local/bin/miniconda/pkgs/gsl-2.7-h93259b0_0
appears to be corrupted. The path 'lib/libgslcblas.0.dylib'
specified in the package manifest cannot be found.

CondaVerificationError: The package for gsl located at /usr/local/bin/miniconda/pkgs/gsl-2.7-h93259b0_0
appears to be corrupted. The path 'lib/libgslcblas.dylib'
specified in the package manifest cannot be found.

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/DECkeysym.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/HPkeysym.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/Sunkeysym.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/X.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/XF86keysym.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/Xatom.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/Xfuncproto.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/ap_keysym.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/keysym.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::xorg-xproto-7.0.31-h35c211d_1007, conda-forge/osx-64::tk-8.6.12-h5dbffcc_0
path: 'include/X11/keysymdef.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::tk-8.6.12-h5dbffcc_0, conda-forge/osx-64::xorg-libx11-1.8.4-hb7f2c08_0
path: 'include/X11/Xlib.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::tk-8.6.12-h5dbffcc_0, conda-forge/osx-64::xorg-libx11-1.8.4-hb7f2c08_0
path: 'include/X11/Xutil.h'

ClobberError: This transaction has incompatible packages due to a shared path.
packages: conda-forge/osx-64::tk-8.6.12-h5dbffcc_0, conda-forge/osx-64::xorg-libx11-1.8.4-hb7f2c08_0
path: 'include/X11/cursorfont.h'

Hi @JESSICA_BROWN,
It looks like something is going awry with your miniconda. I would recommend completely uninstalling miniconda and trying installing it again. (I would try to give you the command but I think the best thing is to look it up for your computer) Let me know if that works!

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That worked thank you!

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