hpages
commented
10 months ago Yes please get rid of the brewed Python3. It's been a while since we don't need it anymore. See https://github.com/Bioconductor/BBS/pull/182#issuecomment-1218903180 (from August 2022).
If it comes back as the dependency of something else that we need to brew, and if the installation is "keg-only", then it should not be a problem because "keg-only" means that it won't be in the PATH. So hopefully we won't need to use brew uninstall --ignore-dependencies, which is something we should not use lightly and only as a very last resort.
We should also put
export PATH=/opt/R/x86_64/bin:$PATHorexport PATH=/opt/R/arm64/bin:$PATHin/etc/profile.
Is this related to Python? If not then maybe we can discuss this in a separate issue?
Thanks
jwokaty
I don't think we need to
brew install pythonanymore as described in https://github.com/Bioconductor/BBS/blob/devel/Doc/Prepare-macOS-Big-Sur-HOWTO.md#211-install-python-3 since tensorflow is now available for newer python versions, so this section in the documentation needs to be rewritten. Maybe it just needs to be a newer version or install the required dependencies (maybe we should also note what packages require them?). We should also putexport PATH=/opt/R/x86_64/bin:$PATHorexport PATH=/opt/R/arm64/bin:$PATHin/etc/profile.Note that brew installing some packages, such as mono and salt may require a version of python to be brew installed and also openssl. In these cases, we should
brew uninstall --ignore-dependencies $PACKAGEfor the package (maybebrew autoremovetoo?). Ifbrew installsymlinks a brewed python, remove the link withbrew unlink $PACKAGE.Note: without a brewed openssl, it seems that pip3 will fail to update because it needs ssl, which is why we should use the default installed python instead.
On merida1, need to
brew uninstall python@3.11andpip3 installdependencies since it is currently showing an ssl error visible at the end ofpip3 list.