If I try to install qiime2-2018.4 next to my existing qiime2-2018.2 installation using conda, I get the following error:
conda env create -n qiime2-2018.4 --file qiime2-2018.4-py35-linux-conda.yml
Solving environment: done
Preparing transaction: done
Verifying transaction: failed
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/aclocal.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/autoheader.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/autom4te.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/automake.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/autoreconf.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/autoscan.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/autoupdate.bak’
specified in the package manifest cannot be found.
CondaVerificationError: The package for vsearch located at /home/christian/miniconda3/pkgs/vsearch-2.7.0-1
appears to be corrupted. The path ‘bin/ifnames.bak’
specified in the package manifest cannot be found.
ClobberWarning: This transaction has incompatible packages due to a shared path.
packages: conda-forge::gettext-0.19.8.1-0, conda-forge::gsl-2.1-2, defaults::libgcc-ng-7.2.0-hdf63c60_3, conda-forge::readline-7.0-0
path: ‘share/info/dir’
ClobberWarning: This transaction has incompatible packages due to a shared path.
packages: defaults::libgfortran-3.0.0-1, defaults::libgcc-7.2.0-h69d50b8_2
path: ‘lib/libgfortran.so.3’
…and this ClobberWarning goes on and on and on for maybe every package?
Things I tried that did not work:
- clearing conda cache
- adding “path_conflict: warn” to a .condarc file
- reinstalling conda
I am pretty sure this has something to do with my python installations in my Ubuntu 16.04 VirtualBox. I tried the installation on an older QIIME2 virtualbox and it worked fine.
Has anyone else seen these errors? Is there a fix for this?
Thanks,
Christian