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rdkit / homebrew-rdkit

Homebrew formula for rdkit
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Pin boost and boost-python3 #73

Closed UnixJunkie closed 4 years ago

UnixJunkie commented 4 years ago

Hello, This should make the rdkit formula much more stable. I did not create the two boost-related formulas (at version 1.70). I just took them from the history of the homebrew-core repository of formulas. The only drawback I see is that the build time for rdkit on macs will significantly increase. But, as a Unix user, I have to admit that seeing something broken today that was working yesterday annoys me a lot. So, having the rdkit homebrew formula being more reproducible is a net advantage. Regards, F.

UnixJunkie commented 4 years ago

should fix https://github.com/rdkit/homebrew-rdkit/issues/50 and addresses https://github.com/rdkit/homebrew-rdkit/issues/65

UnixJunkie commented 4 years ago

There is a risk that the Travis CI will time out. If that happens, we should raise the timeout value. Because, now we have to install boost, plus boost-python3 and rdkit from sources...

UnixJunkie commented 4 years ago

the Travis things also needed an update, tests are underway

cthoyt commented 4 years ago

Thanks for beginning the process to update this. Much appreciated

UnixJunkie commented 4 years ago

We have a problem here: the CI tests go over 50 min so they are stopped no matter what.

UnixJunkie commented 4 years ago

@greglandrum do you want that we fix to a specific version of boost and boost-python3? I just took 1.70 because it looks like the last version that was working in homebrew. If you prefer another specific version, just say so.

UnixJunkie commented 4 years ago

I think this can be merged, at last... @greglandrum the only thing you need to check is that you are OK to pin boost and boost-python3 to 1.70. If you are not OK with that, just tell me which one you want to commit to.

UnixJunkie commented 4 years ago

@mcs07 Hi Matt, can you provide some feedback on this PR?

UnixJunkie commented 4 years ago

There were no dissident voices, so I merged.

cthoyt commented 4 years ago

When installing brew install --head rdkit --with-python3 --with-inchi, it's unable to find the precompiled version of boost. We're having a short discussion on twitter about it right now here:

UnixJunkie commented 4 years ago

When installing brew install --head rdkit --with-python3 --with-inchi, it's unable to find the precompiled version of boost.

Try this:

brew update
which python3 || brew install python3
pip3 install numpy
brew unlink boost || echo boost_not_installed
brew unlink boost-python3 || echo boost-python3_not_installed
brew install rdkit --with-python3 --with-inchi

Send the full log (as a gist) if it doesn't work.

UnixJunkie commented 4 years ago

When installing brew install --head rdkit --with-python3 --with-inchi, it's unable to find the precompiled version of boost. We're having a short discussion on twitter about it right now here:

Recompiling boost is putting my 2011 MBP through quite a work out joy @RDKit_org pic.twitter.com/InsBl1SxGn— Charles Tapley Hoyt (@cthoytp) September 30, 2019

If you want to improve on that (build time), you can work on this issue: https://github.com/rdkit/homebrew-rdkit/issues/74